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headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "acinetobacter infections", "pathogens", "geographical locations", "microbiology", "animals", "genetic mapping", "bacterial diseases", "body lice", "algeria", "insect vectors", "bacteria", "bacterial pa...	Body lice of homeless people reveal the presence of several emerging bacterial pathogens in northern Algeria	journal.pntd.0006397	null	[ [ "Two genera are recognized within the human sucking lice order ( Phthiraptera: Anoplura ) : Pthirus and Pediculus [1 , 2] .", "Each genus is presented by one species: Pthirus pubis and Pediculus humanus , respectively [3 , 4] .", "Both louse species are an obligate blood-feeding parasites that thrived...	[ "Human lice , Pediculus humanus , are obligate blood-sucking parasites .", "Body lice , Pediculus h .", "humanus , occur in two divergent mitochondrial clades ( A and D ) each exhibiting a particular geographic distribution .", "Currently , the body louse is recognized as the only vector for louse-borne disea...	[ "Head lice , Pediculus h .", "capitis , and body lice , Pediculus h .", "humanus , are obligatory blood-sucking ectoparasites .", "The body lice occur in two divergent mitochondrial clades ( A and D ) each exhibiting a particular geographic distribution .", "Currently , the body louse is the only recognized...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "genome sequencing", "genomics", "genetic mutation", "genetics", "biology", "computational biology", "genetics and genomics" ]	Confidence-based Somatic Mutation Evaluation and Prioritization	journal.pcbi.1002714	null	[ [ "Next generation sequencing ( NGS ) has revolutionized our ability to determine genomes and compare , for example , tumor to normal cells to identify somatic mutations .", "However , the platform is not error free and various experimental and algorithmic factors contribute to the false positive rate when ...	[ "Next generation sequencing ( NGS ) has enabled high throughput discovery of somatic mutations .", "Detection depends on experimental design , lab platforms , parameters and analysis algorithms .", "However , NGS-based somatic mutation detection is prone to erroneous calls , with reported validation rates near ...	[ "Next generation sequencing ( NGS ) has enabled unbiased , high throughput discovery of genetic variations and somatic mutations .", "However , the NGS platform is still prone to errors resulting in inaccurate mutation calls .", "A statistical measure of the confidence of putative mutation calls would enable re...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "developmental biology", "cell biology", "genetics and genomics" ]	Dosage Compensation in the Mouse Balances Up-Regulation and Silencing of X-Linked Genes	journal.pbio.0050326	In mouse embryonic stem cells, X:autosome expression balance is achieved by up-regulating X-linked genes in both sexes and gene-by-gene silencing on one female X chromosome.	[ [ "In many higher eukaryotes , sex determination mechanisms have evolved in a way that has generated chromosomal differences between the sexes .", "In eutherian and marsupial mammals and the fruit fly Drosophila , females have two copies of a gene-rich X chromosome , whereas males have one X and one smaller...	[ "Dosage compensation in mammals involves silencing of one X chromosome in XX females and requires expression , in cis , of Xist RNA .", "The X to be inactivated is randomly chosen in cells of the inner cell mass ( ICM ) at the blastocyst stage of development .", "Embryonic stem ( ES ) cells derived from the ICM...	[ "In organisms such as fruit flies and humans , major chromosomal differences exist between the sexes: females have two large , gene-rich X chromosomes , and males have one X and one small , gene-poor Y . Various strategies have evolved to balance X-linked gene expression between the single X and the autosomes , and...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell death", "medicine and health sciences", "autophagic cell death", "nervous system", "cell processes", "brain", "vertebrates", "animals", "animal models", "osteichthyes", "model organisms", "hindbrain", "immunoprecipitation", "neuronal death", "molecular biology techniques", "resea...	A Founder Mutation in VPS11 Causes an Autosomal Recessive Leukoencephalopathy Linked to Autophagic Defects	journal.pgen.1005848	null	[ [ "Genetic leukoencephalopathies ( gLEs ) are a group of heterogeneous disorders with white matter abnormality in the central nervous system ( CNS ) [1 , 2] .", "Patients affected with gLEs manifest variable neurologic phenotypes including motor impairment , hypotonia , pyramidal dysfunction , dystonia and/...	[ "Genetic leukoencephalopathies ( gLEs ) are a group of heterogeneous disorders with white matter abnormalities affecting the central nervous system ( CNS ) .", "The causative mutation in ~50% of gLEs is unknown .", "Using whole exome sequencing ( WES ) , we identified homozygosity for a missense variant , VPS11...	[ "Genetic leukoencephalopathies ( gLEs ) are a group of heterogeneous disorders with white matter abnormalities in the central nervous system ( CNS ) .", "Patients affected with gLEs have brain white matter defects that can be seen on MRI and exhibit variable neurologic phenotypes including motor impairment , hypo...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "computational biology/evolutionary modeling", "computational biology/comparative sequence analysis", "computational biology/sequence motif analysis" ]	CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing	journal.pcbi.1000090	null	[ [ "We concern ourselves with uncovering motifs in eukaryotic cis-regulatory modules ( CRM ) from multiple evolutionarily related species , such as the members from the Drosophila clade .", "Due to high degeneracy of motif instances , and complex motif organization within the CRMs , pattern-matching-based mo...	[ "Functional turnover of transcription factor binding sites ( TFBSs ) , such as whole-motif loss or gain , are common events during genome evolution .", "Conventional probabilistic phylogenetic shadowing methods model the evolution of genomes only at nucleotide level , and lack the ability to capture the evolution...	[ "Functional turnover of transcription factor binding sites ( TFBSs ) , such as whole-motif loss or gain , are common events during genome evolution , and play a major role in shaping the genome and regulatory circuitry of contemporary species .", "Conventional methods for searching non-conserved motifs across evo...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "blood cells", "ecology and environmental sciences", "vertebrates", "animals", "mammals", "epithelial cells", "animal models", "eukaryotic cells", "histology", "chemical ecology", "model organisms", "veterinary science", "research and analysis methods", "animal cells", "biological tissue...	Insights into Embryo Defenses of the Invasive Apple Snail Pomacea canaliculata: Egg Mass Ingestion Affects Rat Intestine Morphology and Growth	journal.pntd.0002961	null	[ [ "The invasive apple snail Pomacea canaliculata ( Lamarck , 1822 ) ( Architaenioglossa , Ampullariidae ) has become a serious aquatic crop pest in Asia and a vector of the rat lungworm Angiostrongylus cantonensis that causes human eosinophilic meningitis , a potentially fatal disease considered an emerging inf...	[ "The spread of the invasive snail Pomacea canaliculata is expanding the rat lungworm disease beyond its native range .", "Their toxic eggs have virtually no predators and unusual defenses including a neurotoxic lectin and a proteinase inhibitor , presumably advertised by a warning coloration .", "We explored th...	[ "Filled with nutritious substances to nourish the embryos , eggs of most animals are often the targets of pathogens and predators .", "An exception are the eggs of Pomacea canaliculata –known as the apple snail– which have hardly any predators .", "This freshwater snail is a serious aquatic crop pest in several...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Transhydrogenase Promotes the Robustness and Evolvability of E. coli Deficient in NADPH Production	journal.pgen.1005007	null	[ [ "Metabolic networks , consisting of metabolites connected through biochemical reactions , are central to life by extracting energy from nutrients and converting chemicals into building blocks of organisms .", "Similar to the architecture of the Internet and other biological networks ( e . g . gene regulat...	[ "Metabolic networks revolve around few metabolites recognized by diverse enzymes and involved in myriad reactions .", "Though hub metabolites are considered as stepping stones to facilitate the evolutionary expansion of biochemical pathways , changes in their production or consumption often impair cellular physio...	[ "The structure of biological networks , like traffic systems or the Internet , features few hubs connected by numerous components .", "Though the conservation and high connectivity of hubs serve as key junctions to promote network expansion , addition or removal of connections surrounding hubs may disturb the who...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "allosteric regulation", "chemical bonding", "crystal structure", "markov models", "statistics", "condensed matter physics", "enzymology", "simulation and modeling", "multivariate analysis", "mathematics", "artificial intelligence", "crystallography", "enzyme chemistry", "physical chemistr...	Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis	journal.pcbi.1006801	null	[ [ "Light , oxygen , or voltage ( LOV ) domains are small , commutable elements that couple blue-light activation to protein conformational changes for blue-light responses in bacteria , archaea , fungi and plants .", "One common feature shared by all LOV domains is that a cofactor , flavin adenine dinucleot...	[ "The fungal circadian clock photoreceptor Vivid ( VVD ) contains a photosensitive allosteric light , oxygen , voltage ( LOV ) domain that undergoes a large N-terminal conformational change .", "The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains uncle...	[ "Allostery is an important but elusive property that governs critical functionality of many proteins .", "Quantitative analysis is needed to provide significant insight into protein allostery and lead to better prediction power of this ubiquitous phenomenon .", "We developed machine learning methods based on ro...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	Active Surveillance of Hansen's Disease (Leprosy): Importance for Case Finding among Extra-domiciliary Contacts	journal.pntd.0002093	null	[ [ "Hansen's disease , as leprosy is called in Brazil , is an infectious disease of insidious onset , caused by Mycobacterium leprae .", "[1]–[3] Transmission is thought to occur primarily via the airborne route from people with multibacillary disease .", "A great challenge to disease control is the iden...	[ "Hansen's disease ( leprosy ) remains an important health problem in Brazil , where 34 , 894 new cases were diagnosed in 2010 , corresponding to 15 . 3% of the world's new cases detected in that year .", "The purpose of this study was to use home visits as a tool for surveillance of Hansen's disease in a hyperend...	[ "Hansen's Disease , or leprosy , is a disease that despite curative therapy is still a health problem in many areas , particularly in Brazil , which has a high new case detection rate .", "If symptoms of Hansen's disease are not recognized , delay in diagnosis can result in severe disability .", "Within the sta...	2013
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "immune activation", "retrovirology and hiv immunopathogenesis", "immunity to infections", "immunology", "adaptive immunity", "immune defense", "infectious disease control", "infectious diseases", "hiv", "immune response", "clinical immunology", "immunity", "viral diseases" ]	Post-Treatment HIV-1 Controllers with a Long-Term Virological Remission after the Interruption of Early Initiated Antiretroviral Therapy ANRS VISCONTI Study	journal.ppat.1003211	null	[ [ "HIV-1 infection is normally characterized by sustained viral replication and a progressive loss of CD4+ T cells , leading to AIDS .", "Combined antiretroviral therapy ( cART ) suppresses viral replication and drastically reduces morbidity and mortality [1] .", "However , cART does not eradicate infec...	[ "Combination antiretroviral therapy ( cART ) reduces HIV-associated morbidities and mortalities but cannot cure the infection .", "Given the difficulty of eradicating HIV-1 , a functional cure for HIV-infected patients appears to be a more reachable short-term goal .", "We identified 14 HIV patients ( post-trea...	[ "There is a renewed scientific interest in developing strategies allowing long-term remission in HIV-1-infected individuals .", "Very rare ( <1% ) patients are able to spontaneously control viremia to undetectable levels ( HIV controllers , HICs ) .", "However , the possibility to translate their mechanisms of ...	2013
[ "Introduction", "Methods", "Results/ Discussion", "Conclusion and Outlook" ]	[]	Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery	journal.pcbi.1004074	null	[ [ "Drug discovery faces important challenges in terms of cost , complexity and the amount of time required to yield promising compounds .", "To avoid side effects , a valuable drug precursor must have high affinity with the target protein while minimizing interactions with other proteins .", "Unfortunat...	[ "The discovery of peptides possessing high biological activity is very challenging due to the enormous diversity for which only a minority have the desired properties .", "To lower cost and reduce the time to obtain promising peptides , machine learning approaches can greatly assist in the process and even partly...	[ "Part of the complexity of drug discovery is the sheer chemical diversity to explore combined to all requirements a compound must meet to become a commercial drug .", "Hence , it makes sense to automate this chemical exploration endeavor in a wise , informed , and efficient fashion .", "Here , we focused on pep...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	A Fusion-Inhibiting Peptide against Rift Valley Fever Virus Inhibits Multiple, Diverse Viruses	journal.pntd.0002430	null	[ [ "Rift Valley fever ( RVF ) is a disease of major public health and economic concern , affecting humans and livestock throughout Africa [1]–[6] and the Arabian Peninsula [7] .", "The etiological agent of this zoonosis , Rift Valley fever virus ( RVFV ) , is an arbovirus belonging to the Phlebovirus genus i...	[ "For enveloped viruses , fusion of the viral envelope with a cellular membrane is critical for a productive infection to occur .", "This fusion process is mediated by at least three classes of fusion proteins ( Class I , II , and III ) based on the protein sequence and structure .", "For Rift Valley fever virus...	[ "Entry into a cell is an essential stage of the viral replication cycle .", "Enveloped viruses require fusion of viral and cellular membranes for the viral genome to enter the cell cytoplasm .", "This entry is mediated by a viral fusion protein .", "Here , we synthesized peptides based on the Rift Valley feve...	2013
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "urology", "medicine and health sciences", "innate immune system", "immune physiology", "cytokines", "helminths", "immunology", "parasitic diseases", "animals", "vaccines", "preventive medicine", "developmental biology", "sexually ...	An investigation into the role of chronic Schistosoma mansoni infection on Human Papillomavirus (HPV) vaccine induced protective responses	journal.pntd.0007704	null	[ [ "Human Papillomavirus ( HPV ) remains one of the most common sexually transmitted viruses in the world and is responsible for cervical cancer .", "Cervical cancer has been categorized as the 3rd most common cancer affecting women in the world .", "It has been estimated that 527 , 624 women are diagnos...	[ "Schistosoma mansoni is one of the most common helminth infections affecting a large population of people in sub-Saharan Africa .", "This helminth infection is known to cause immunomodulation which has affected the efficacy of a number of vaccines .", "This study examined whether a chronic schistosoma infection...	[ "In sub-Saharan Africa countries , vaccines are administered to people who may suffer from existing infections , especially helminth infections .", "These infections are known to modulate immune responses rendering some vaccines ineffective .", "The impact of helminth infections such as schistosomiasis on a rec...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "velocity", "acceleration", "medicine and health sciences", "legs", "classical mechanics", "limbs (anatomy)", "biological locomotion", "biomechanics", "surgical and invasive medical procedures", "functional electrical stimulation", "research and analysis methods", "musculoskeletal system", "...	Evaluation of the Phase-Dependent Rhythm Control of Human Walking Using Phase Response Curves	journal.pcbi.1004950	null	[ [ "Humans and animals control their walking rhythms to maintain their motion in a variable environment .", "When swing motion is disturbed during early swing phase , flexor muscles are evoked and swing phase is prolonged , and disturbance late in swing phase evokes extensor muscles , advancing touch-down ( ...	[ "Humans and animals control their walking rhythms to maintain motion in a variable environment .", "The neural mechanism for controlling rhythm has been investigated in many studies using mechanical and electrical stimulation .", "However , quantitative evaluation of rhythm variation in response to perturbation...	[ "Humans and animals tune their walking rhythms when motion is disturbed , such that they hesitate before making the transition from stance to swing phase .", "The effectiveness of rhythm control for stability has also been shown , and thus the elucidation of rhythm responses is important to understanding human st...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases", "medicine and health sciences", "biology and life sciences", "immunology", "parasitic diseases" ]	Leishmania Specific CD4 T Cells Release IFNγ That Limits Parasite Replication in Patients with Visceral Leishmaniasis	journal.pntd.0003198	null	[ [ "Visceral leishmaniasis is a chronic disease caused by the protozoan parasites Leishmania donovani and Leishmania infantum/chagasi .", "Leishmania are transmitted by the bite of phlebotomine sand flies , and replicate within macrophages of their mammalian hosts .", "In VL , the target organs are chief...	[ "Visceral leishmaniasis ( VL ) is associated with increased circulating levels of multiple pro-inflammatory cytokines and chemokines , including IL-12 , IFNγ , and TNFα , and elevated expression of IFNγ mRNA in lesional tissue such as the spleen and bone marrow .", "However , an immunological feature of VL patien...	[ "Our research aims to understand the immune failure underlying progression of human visceral leishmaniasis ( VL ) .", "A key immunological feature of VL patients is that their peripheral blood mononuclear cells ( PBMCs ) do not respond to stimulation with leishmanial antigen .", "Surprisingly , when employing a...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "cryptococcus neoformans", "medicine and health sciences", "aspergillus fumigatus", "cryptococcus", "classical mechanics", "pathology and laboratory medicine", "aspergillus", "fungal genetics", "gene regulation", "pathogens", "microbiology", "mechanical stress", "fungi", "model organisms",...	Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans	journal.pgen.1006667	null	[ [ "Ca2+ signaling cascades are employed by eukaryotic cells to control gene expression and other cellular processes .", "Calcineurin is a highly conserved Ca2+/calmodulin-dependent serine/threonine-specific protein phosphatase that plays a central role in orchestrating cellular responses to Ca2+ signaling i...	[ "Calcineurin is a highly conserved Ca2+/calmodulin-dependent serine/threonine-specific protein phosphatase that orchestrates cellular Ca2+ signaling responses .", "In Cryptococcus neoformans , calcineurin is activated by multiple stresses including high temperature , and is essential for stress adaptation and vir...	[ "The ubquitiously conserved serine/threonine-specific protein phosphatase calcineurin is crucial for virulence of several opportunistic human fungal pathogens including Candida albicans , Aspergillus fumigatus , and Cryptococcus neoformans .", "We show that Crz1 acts downstream of calcineurin , to", "1 ) govern...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/innate immunity", "genetics and genomics/genetics of the immune system" ]	Phosphorylation of the Conserved Transcription Factor ATF-7 by PMK-1 p38 MAPK Regulates Innate Immunity in Caenorhabditis elegans	journal.pgen.1000892	null	[ [ "Studies of innate immunity in phylogenetically diverse organisms have revealed the conservation of key signaling pathways mediating pathogen defense [1] , [2] .", "In mammals , the initial encounter between cells of the immune system and pathogenic bacteria triggers the activation of the innate immune re...	[ "Innate immunity in Caenorhabditis elegans requires a conserved PMK-1 p38 mitogen-activated protein kinase ( MAPK ) pathway that regulates the basal and pathogen-induced expression of immune effectors .", "The mechanisms by which PMK-1 p38 MAPK regulates the transcriptional activation of the C . elegans immune re...	[ "We have investigated mechanisms of how the soil nematode Caenorhabditis elegans interacts with pathogenic bacteria .", "Previously , we have established that a conserved PMK-1 p38 mitogen-activated protein kinase ( MAPK ) pathway regulates immunity in C . elegans , establishing the conservation of key innate imm...	2010
[ "Introduction", "Methods", "Results and discussion", "Conclusion" ]	[ "chemical bonding", "protein interactions", "protein structure prediction", "protein structure", "research and analysis methods", "physical chemistry", "proteins", "biological databases", "chemistry", "cross-linking", "proteomics", "molecular biology", "proteasomes", "protein structure com...	Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets	journal.pcbi.1005625	null	[ [ "Many proteins assemble into large macromolecular complexes with essential cellular functions .", "The three dimensional arrangement of proteins in a complex is vital to the complex’s function and knowledge of this arrangement would be highly valuable in understanding the mechanism of function .", "Co...	[ "Determining the three dimensional arrangement of proteins in a complex is highly beneficial for uncovering mechanistic function and interpreting genetic variation in coding genes comprising protein complexes .", "There are several methods for determining co-complex interactions between proteins , among them co-f...	[ "Proteins physically associate into complexes in order to carry out the essential functions of life .", "Knowing how proteins are physically arranged three dimensionally in these complexes provides clues towards how they work .", "In principle , the associations between proteins in large-scale proteomics datase...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "immunology", "biology", "microbiology", "molecular cell biology", "biophysics" ]	Broadly Neutralizing Antibody PGT121 Allosterically Modulates CD4 Binding via Recognition of the HIV-1 gp120 V3 Base and Multiple Surrounding Glycans	journal.ppat.1003342	null	[ [ "The discovery of novel monoclonal antibodies capable of neutralizing a broad spectrum of HIV-1 isolates of various clades ( broadly neutralizing antibodies , bnAbs ) has rapidly accelerated in the past three years and provided valuable new reagents and opportunities for HIV vaccine design [1] , [2] , [3] , [...	[ "New broad and potent neutralizing HIV-1 antibodies have recently been described that are largely dependent on the gp120 N332 glycan for Env recognition .", "Members of the PGT121 family of antibodies , isolated from an African donor , neutralize ∼70% of circulating isolates with a median IC50 less than 0 . 05 µg...	[ "An estimated 33 million adults and children currently live with the human immunodeficiency virus type 1 ( HIV-1 ) , which represents a global prevalence of 0 . 8% .", "In the absence of a cure , the development of a protective vaccine is the long sought-after goal in containment of the pandemic .", "HIV-1 Env ...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	A Library of Plasmodium vivax Recombinant Merozoite Proteins Reveals New Vaccine Candidates and Protein-Protein Interactions	journal.pntd.0004264	null	[ [ "Plasmodium vivax causes an estimated 70–391 million cases of malaria each year [1 , 2] , but is relatively neglected in research programs compared to the more deadly P . falciparum .", "While P . vivax malaria is often considered benign , this description is challenged by a growing body of evidence that ...	[ "A vaccine targeting Plasmodium vivax will be an essential component of any comprehensive malaria elimination program , but major gaps in our understanding of P . vivax biology , including the protein-protein interactions that mediate merozoite invasion of reticulocytes , hinder the search for candidate antigens ."...	[ "Plasmodium vivax causes malaria in millions of people each year , primarily in Southeast Asia and Central and South America .", "P . vivax has a dormant liver stage , which can lead to disease recurrence in infected individuals even in the absence of mosquito transmission .", "The development of vaccines that ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "plant microbiology", "viruslike particles", "proteins", "viral transmission and infection", "virology", "macromolecular assemblies", "biology", "microbiology" ]	The Stable Association of Virion with the Triple-gene-block Protein 3-based Complex of Bamboo mosaic virus	journal.ppat.1003405	null	[ [ "Plant viruses spread their genomes from infected cell to uninfected cell via plasmodesmata ( PD ) with the assistance of virus-encoded movement proteins .", "Some RNA viruses , like those in Virgaviridae [1] and Flexiviridae [2] families , encode three movement proteins organized into a triple gene block...	[ "The triple-gene-block protein 3 ( TGBp3 ) of Bamboo mosaic virus ( BaMV ) is an integral endoplasmic reticulum ( ER ) membrane protein which is assumed to form a membrane complex to deliver the virus intracellularly .", "However , the virus entity that is delivered to plasmodesmata ( PD ) and its association wit...	[ "Plant viruses spread their infectious entities from cell to cell via plasmodesmata ( PD ) through the assistance of virus-encoded movement proteins and host factors .", "Some RNA viruses encode three functionally coordinated movement proteins organized into a triple gene block ( TGB ) to facilitate their cell-to...	2013
[ "Results", "Discussion", "Materials and methods" ]	[ "molecular probe techniques", "enzymes", "enzymology", "immunoblotting", "ubiquitin ligases", "fungi", "model organisms", "experimental organism systems", "molecular biology techniques", "chemical dissociation", "ligases", "schizosaccharomyces", "research and analysis methods", "proteins",...	Trade-off and flexibility in the dynamic regulation of the cullin-RING ubiquitin ligase repertoire	journal.pcbi.1005869	null	[ [ "We first examined how the presence of Cand1 affects the steady state occupancies of different SCF complexes ( i . e . Cul1 . SR1 and Cul1 . SR2 ) .", "To this end , we assumed that Cul1 is saturated with SRs , i . e . we considered the physiologically relevant regime SRT = SR1T + SR2T > Cul1T .", "Fr...	[ "Cullin-RING ubiquitin ligases ( CRLs ) catalyze the ubiquitylation of substrates many of which are degraded by the 26S proteasome .", "Their modular architecture enables recognition of numerous substrates via exchangeable substrate receptors that competitively bind to a cullin scaffold with high affinity .", "...	[ "Cullin-RING ubiquitin ligases ( CRLs ) are multisubunit protein complexes where exchangeable substrate receptors ( SRs ) assemble on a cullin scaffold to mediate ubiquitylation and subsequent degradation of a large variety of substrates .", "In humans there are hundreds of different CRLs having potentially thous...	2017
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "rna interference", "plant biology", "crop genetics", "plant science", "plant genomics", "epigenetics", "plants", "flowering plants", "gene expression", "plant genetics", "biology", "dna modification", "plant evolution", "genetics", "genetics and genomics" ]	Role of Transposon-Derived Small RNAs in the Interplay between Genomes and Parasitic DNA in Rice	journal.pgen.1002953	null	[ [ "RNA silencing is a mechanism mediated by small RNAs that regulates gene expression in eukaryotes at both the transcriptional and post-transcriptional levels .", "RNA silencing has a wide range of essential functions in cellular processes necessary for development of animals and plants , and it also has a...	[ "RNA silencing is a defense system against “genomic parasites” such as transposable elements ( TE ) , which are potentially harmful to host genomes .", "In plants , transcripts from TEs induce production of double-stranded RNAs ( dsRNAs ) and are processed into small RNAs ( small interfering RNAs , siRNAs ) that ...	[ "Transposons , which are sometimes referred to as “genomic parasites , ” are a major component of eukaryotic genomes .", "Because transposon activity is often detrimental to host genome stability , most transposons are silenced by the host's defense machinery .", "The mechanisms of transposon silencing , such a...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "immunity to infections", "immunology", "microbiology", "cytomegalovirus infection", "immune defense", "infectious diseases", "viral immune evasion", "biology", "immune response", "immunity", "virology", "innate immunity", "co-infections", "viral diseases" ]	Natural Killer Cell Dependent Within-Host Competition Arises during Multiple MCMV Infection: Consequences for Viral Transmission and Evolution	journal.ppat.1003111	null	[ [ "It is becoming increasingly clear that many infections are caused by multiple distinct strains of the infecting pathogen .", "A recent review documented 51 infections of humans in which there is definitive evidence of such multi-strain infection [1] .", "This is likely to be an underestimation of the...	[ "It is becoming increasingly clear that many diseases are the result of infection from multiple genetically distinct strains of a pathogen .", "Such multi-strain infections have the capacity to alter both disease and pathogen dynamics .", "Infection with multiple strains of human cytomegalovirus ( HCMV ) is com...	[ "Infection of the host with multiple strains of a pathogen is common and occurs with the herpesvirus , human cytomegalovirus ( HCMV ) .", "However the effects of multi-strain infection on the host and the pathogen remain poorly studied .", "Here we show , in a mouse model , that infection of C57BL/6 mice with m...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Rapidly Evolving Genes Are Key Players in Host Specialization and Virulence of the Fungal Wheat Pathogen Zymoseptoria tritici (Mycosphaerella graminicola)	journal.ppat.1005055	null	[ [ "Host specialization of pathogens can be a strong driver of diversification and speciation [1] .", "Host-driven speciation implies the specialization of traits involved in host interactions from the initial infection and the defeat of host defenses to within-host nutrient uptake , multiplication and repro...	[ "The speciation of pathogens can be driven by divergent host specialization .", "Specialization to a new host is possible via the acquisition of advantageous mutations fixed by positive selection .", "Comparative genome analyses of closely related species allows for the identification of such key substitutions ...	[ "Zymoseptoria spp provides a unique model system to study the underlying genetics of host specialization of plant pathogens .", "Closely related Zymoseptoria species , including the prominent wheat pathogen Z . tritici , have recently specialized to distinct grass hosts .", "Positively selected substitutions ha...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "medical doctors", "medical personnel", "tropical diseases", "geographical locations", "parasitic diseases", "health care", "bacterial diseases", "health care providers", "neglected tropical diseases", "onchocerciasis", "africa", "morbidity", "infectious dis...	Neglected tropical disease as a ‘biographical disruption’: Listening to the narratives of affected persons to develop integrated people centred care in Liberia	journal.pntd.0007710	null	[ [ "This study draws significantly on the use of narrative and intersectional theory and combines these approaches to focus on exploration of individual illness experience , how this varies by individual’s diverse social realities , and how the merging of these theoretical approaches can support the development ...	[ "Integrated disease management , disability and inclusion ( DMDI ) for NTDs is increasingly prioritised .", "There is limited evidence on the effectiveness of integrated DMDI from the perspective of affected individuals and how this varies by differing axes of inequality such as age , gender , and disability .", ...	[ "We used narrative methods to consider how individuals’ unique positions of power and privilege shaped their illness experience , to explore what practical and feasible steps could support neglected tropical disease ( NTDs ) programmes to respond to patient need in Liberia and beyond .", "We asked 27 people livin...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "population dynamics", "population biology", "biology" ]	Sexuality Generates Diversity in the Aflatoxin Gene Cluster: Evidence on a Global Scale	journal.ppat.1003574	null	[ [ "Aspergillus flavus and A . parasiticus are important fungal colonizers of food crops as well as pathogens of animals and produce the carcinogenic aflatoxins of which aflatoxin B1 is the most carcinogenic natural compound known [1] , [2] .", "The two species occur in soil and drought stress in plant hosts...	[ "Aflatoxins are produced by Aspergillus flavus and A . parasiticus in oil-rich seed and grain crops and are a serious problem in agriculture , with aflatoxin B1 being the most carcinogenic natural compound known .", "Sexual reproduction in these species occurs between individuals belonging to different vegetative...	[ "Fungal pathogen populations have mixed proportions of vegetative propagation and sexual reproduction ranging from predominantly clonal to varying levels of sexuality .", "Aflatoxins are the most potent naturally occurring carcinogens known and aflatoxin-producing Aspergillus flavus and A . parasiticus show exten...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "global health" ]	Addressing the Neglected Tropical Disease Podoconiosis in Northern Ethiopia: Lessons Learned from a New Community Podoconiosis Program	journal.pntd.0001560	null	[ [ "Podoconiosis , or non-filarial elephantiasis , is a geochemical type of neglected tropical disease that affects individuals , often barefoot subsistence farmers , exposed to the red clay soil originating from volcanic rock [1] .", "Irritant particles in this soil penetrate the skin of the foot resulting ...	[ "Despite its great public health importance , few control initiatives addressing podoconiosis ( non-filarial elephantiasis , a geochemical neglected tropical disease ) exist .", "In June 2010 , the first podoconiosis program in Northern Ethiopia , consisting of prevention , awareness , and care and support activi...	[ "Podoconiosis is a chronic non-infectious disease that causes leg swelling among those living and walking bare-footed in red clay soil areas .", "It can be prevented and treated primarily by the use of shoes and foot hygiene .", "In Ethiopia , it is estimated that nearly 11 million people are at risk but few co...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "gene regulation", "regulatory networks", "molecular genetics", "biology", "computational biology" ]	An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors	journal.pcbi.1002603	null	[ [ "The operation of a functioning living cell depends on its ability to tightly regulate its different pathways .", "Most of this regulation is done by proteins that control the function of many other genes ( or themselves in the case of autoregulation ) .", "Transcription factors ( TFs ) are the most a...	[ "Traditionally the gene expression pathway has been regarded as being comprised of independent steps , from RNA transcription to protein translation .", "To date there is increasing evidence of coupling between the different processes of the pathway , specifically between transcription and splicing .", "To stud...	[ "The operation of a living cell depends on its ability to regulate its different functions .", "The master regulators in the cell are proteins , which control the function of many other genes by several mechanisms .", "Transcription factors can differentially activate or repress the transcription of genes by bi...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Interferon-γ Inhibits Ebola Virus Infection	journal.ppat.1005263	null	[ [ "Ebola virus ( EBOV ) is a member of the genus Ebolavirus within the Filoviridae family of highly pathogenic viruses .", "These viruses cause a severe hemorrhagic fever syndrome in humans and non-human primates ( NHP ) .", "EBOV infection frequently is associated with high mortality rates and is respo...	[ "Ebola virus outbreaks , such as the 2014 Makona epidemic in West Africa , are episodic and deadly .", "Filovirus antivirals are currently not clinically available .", "Our findings suggest interferon gamma , an FDA-approved drug , may serve as a novel and effective prophylactic or treatment option .", "Using...	[ "Filovirus outbreaks occur sporadically , but with increasing frequency .", "With no current approved filovirus therapeutics , the 2014 Makona Ebola virus epidemic in Guinea , Sierra Leone and Liberia emphasizes the need for effective treatments against this highly pathogenic family of viruses .", "The use of t...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "immune physiology", "crystal structure", "respiratory infections", "enzyme-linked immunoassays", "viral transmission and infection", "immunology", "condensed matter physics", "microbiology", "pulmonology", "epithelial cells", "preventive medicine", "viral att...	Structural basis for recognition of the central conserved region of RSV G by neutralizing human antibodies	journal.ppat.1006935	null	[ [ "Human respiratory syncytial virus ( RSV ) infects nearly all children by the age of two [1] .", "Although RSV does not typically cause severe disease in healthy adults , it is a major pathogen for infants , the elderly , and immunocompromised individuals , with a propensity to cause severe lower respirat...	[ "Respiratory syncytial virus ( RSV ) is a major cause of severe lower respiratory tract infections in infants and the elderly , and yet there remains no effective treatment or vaccine .", "The surface of the virion is decorated with the fusion glycoprotein ( RSV F ) and the attachment glycoprotein ( RSV G ) , whi...	[ "Respiratory syncytial virus ( RSV ) is a common cause of bronchiolitis and pneumonia , and is a leading cause of infant deaths globally due to infectious disease .", "Despite decades of research , there is still no vaccine or widespread treatment for RSV .", "In this study , we isolated two antibodies that bin...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Identification of Novel Compounds Inhibiting Chikungunya Virus-Induced Cell Death by High Throughput Screening of a Kinase Inhibitor Library	journal.pntd.0002471	null	[ [ "Chikungunya virus ( CHIKV ) is a mosquito-borne pathogen belonging to the Semliki Forest antigenic complex of the genus Alphavirus , family Togaviridae [1] .", "CHIKV has a single , positive strand linear RNA genome of approximately 11 . 7 kb and is comprised of two open reading frames ( ORF ) : a 5′ non...	[ "Chikungunya virus ( CHIKV ) is a mosquito-borne arthrogenic alphavirus that causes acute febrile illness in humans accompanied by joint pains and in many cases , persistent arthralgia lasting weeks to years .", "The re-emergence of CHIKV has resulted in numerous outbreaks in the eastern hemisphere , and threaten...	[ "Recent outbreaks and expanding global distribution of Chikungunya virus ( CHIKV ) in different regions of Asia , Africa and Europe necessitates the development of effective therapeutic interventions .", "At present , only two antiviral compounds ( chloroquine and ribavirin ) that inhibit viral infection in vitro...	2013
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "biochemistry", "evolutionary biology", "pharmacology", "chemical biology", "genetics and genomics", "eubacteria" ]	Bioassay-Guided Evolution of Glycosylated Macrolide Antibiotics in Escherichia coli	journal.pbio.0050045	An erythromycin-producingE. coli recombinant strain with an antibiotic-overproducing mutation in the mycarose biosynthesis pathway produced second-generation mutants capable of directed biosynthesis of enhanced precursor macrolide antibiotics.	[ [ "Polyketides are a diverse and clinically important class of natural products which exhibit anti-infective , antitumor , immunosuppressive , and cholesterol-lowering properties , among others [1] .", "The modular architecture of polyketide synthases provides an attractive scaffold for biosynthetic enginee...	[ "Macrolide antibiotics such as erythromycin are clinically important polyketide natural products .", "We have engineered a recombinant strain of Escherichia coli that produces small but measurable quantities of the bioactive macrolide 6-deoxyerythromycin D . Bioassay-guided evolution of this strain led to the ide...	[ "The antibacterial activity of erythromycin , an important polyketide antibiotic precursor , requires the transfer of two unusual sugars called mycarose and desosamine ( both glycosyl groups ) , onto the nonsugar part of the glycoside molecule ( macrocyclic aglycone ) .", "We reconstituted the biosynthetic pathwa...	2007
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "reverse transcriptase-polymerase chain reaction", "taxonomy", "dengue virus", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "tropical diseases", "microbiology", "rna extraction", "geographical locations", "indonesia", "viruses", "phylogenetics", "data m...	Dengue in Bali: Clinical characteristics and genetic diversity of circulating dengue viruses	journal.pntd.0005483	null	[ [ "Dengue is the most important arthropod-borne disease affecting humans with high incidence in tropical and subtropical countries .", "It is estimated that 390 million infections occur annually and over 70% of the world population is at risk of being infected by dengue viruses ( DENVs ) [1] .", "Dengue...	[ "A high number of dengue cases are reported annually in Bali .", "Despite the endemicity , limited data on dengue is available for Bali localities .", "Molecular surveillance study was conducted to explore the clinical and virological characteristics of dengue patients in urban Denpasar and rural Gianyar areas ...	[ "Dengue is the most significant mosquito-borne viral disease affecting humans .", "Up to one third of the world population is at risk of dengue virus ( DENV ) infection , transmitted through the bite of Aedes mosquitoes .", "Bali , a well-known international tourist destination , is regularly ravaged by dengue ...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Outcome after Discontinuing Long-Term Benzimidazole Treatment in 11 Patients with Non-resectable Alveolar Echinococcosis with Negative FDG-PET/CT and Anti-EmII/3-10 Serology	journal.pntd.0003964	null	[ [ "Alveolar echinococcosis ( AE ) , one of the most Iethal human helminthic infections , is acquired by ingestion of eggs from Echinococcus multilocularis .", "AE behaves biologically like a malignant tumor with a tendency to metastasize into distant organs [1–5] .", "The treatment of choice is radical ...	[ "Benzimidazoles are efficacious for treating non-resectable alveolar echinococcosis ( AE ) , but their long-term parasitocidal ( curative ) effect is disputed .", "In this study , we prospectively analyzed the potential parasitocidal effect of benzimidazoles and whether normalization of FDG-PET/CT scans and anti-...	[ "Alveolar echinococcosis is one of the mostly deadly human parasitic diseases if left untreated .", "The treatment of choice is surgical resection , followed by two years of benzimidazole treatment .", "Unfortunately , only about 30–40% of patients have a resectable disease , while the others require medical tr...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	IL-10 Blocks the Development of Resistance to Re-Infection with Schistosoma mansoni	journal.ppat.1002171	null	[ [ "Despite inexpensive and effective chemotherapy , schistosomiasis continues to plague sub-Saharan Africa , south-east Asia , south America and areas of the Caribbean .", "This is due , in part , to rapid re-infection rates following curative chemotherapy .", "Recent estimates indicate that 200 million...	[ "Despite effective chemotherapy to treat schistosome infections , re-infection rates are extremely high .", "Resistance to reinfection can develop , however it typically takes several years following numerous rounds of treatment and re-infection , and often develops in only a small cohort of individuals .", "Us...	[ "Schistosomes are zoonotic parasitic helminths that infect hundreds of millions of people worldwide .", "Despite effective chemotherapy , schistosomiasis- the disease caused by these parasites , still plagues tropical regions of the world .", "This is due , in part , to poor resistance to reinfection resulting ...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "protein interactions", "nmr spectroscopy", "electricity", "parasitic diseases", "parasitic protozoans", "spectrins", "organisms", "electrostatics", "protozoans", "red blood cells", "cellular structures and organelles", "cytoskeleton", "rese...	Structural analysis of P. falciparum KAHRP and PfEMP1 complexes with host erythrocyte spectrin suggests a model for cytoadherent knob protrusions	journal.ppat.1006552	null	[ [ "Malaria remains one of the most lethal global diseases , causing an estimated 429 , 000 deaths in 2016 [1] .", "The majority of these deaths are attributed to infections by the Plasmodium falciparum parasite ( reviewed in [2] ) .", "Compared to other human-infective Plasmodia , P . falciparum is dist...	[ "Plasmodium falciparum Erythrocyte Membrane Protein 1 ( PfEMP1 ) and Knob-associated Histidine-rich Protein ( KAHRP ) are directly linked to malaria pathology .", "PfEMP1 and KAHRP cluster on protrusions ( knobs ) on the P . falciparum-infected erythrocyte surface and enable pathogenic cytoadherence of infected e...	[ "Formation of cytoadherent knobs on the surface of P . falciparum infected erythrocytes correlates with malaria pathology .", "Two parasite proteins central for knob formation and cytoadherence , KAHRP and PfEMP1 , have previously been shown to bind the erythrocyte cytoskeleton .", "Both KAHRP and PfEMP1 includ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "veterinary pathology", "veterinary diseases", "agriculture", "veterinary virology", "aquaculture", "biology and life sciences", "veterinary science", "shrimp farming" ]	An Invertebrate Warburg Effect: A Shrimp Virus Achieves Successful Replication by Altering the Host Metabolome via the PI3K-Akt-mTOR Pathway	journal.ppat.1004196	null	[ [ "The Warburg effect , which was first described by Warburg in the 1930s , is a metabolic rerouting used by tumor cells and cancer cells to support their high energy requirements and high rates of macromolecular synthesis [1] , [2] .", "In cancer cells , the main hallmark of the Warburg effect is aerobic g...	[ "In this study , we used a systems biology approach to investigate changes in the proteome and metabolome of shrimp hemocytes infected by the invertebrate virus WSSV ( white spot syndrome virus ) at the viral genome replication stage ( 12 hpi ) and the late stage ( 24 hpi ) .", "At 12 hpi , but not at 24 hpi , th...	[ "The Warburg effect ( or aerobic glycolysis ) is a metabolic shift that was first found in cancer cells , but has also recently been discovered in vertebrate cells infected by viruses .", "The Warburg effect facilitates the production of more energy and building blocks to meet the enormous biosynthetic requiremen...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	sRNA-Mediated Regulation of P-Fimbriae Phase Variation in Uropathogenic Escherichia coli	journal.ppat.1005109	null	[ [ "Uropathogenic E . coli ( UPEC ) are a group of genetically heterogeneous isolates [1] known to display a complex infection cycle within their host .", "In the course of acute cystitis , UPEC invade the superficial bladder epithelial cells and replicate in the host cell cytoplasm to form intracellular bac...	[ "Uropathogenic Escherichia coli ( UPEC ) are capable of occupying physiologically distinct intracellular and extracellular niches within the urinary tract .", "This feat requires the timely regulation of gene expression and small RNAs ( sRNAs ) are known to mediate such rapid adjustments in response to changing e...	[ "Recent years have seen an increasing emphasis placed on the role of small RNAs ( sRNAs ) in the regulation of bacterial gene expression and stress adaptation .", "The advent of high-throughput sequencing methods has now made it possible to directly monitor the appearance of potentially virulence-associated sRNAs...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "neurodegenerative diseases", "brain", "neuroscience", "animal models", "synaptic plasticity", "model organisms", "experimental organism systems", "genome analysis", "cerebellum", "research and analysis methods", "developmental neuroscience", "genomics", "dy...	Mutations in THAP1/DYT6 reveal that diverse dystonia genes disrupt similar neuronal pathways and functions	journal.pgen.1007169	null	[ [ "Dystonia is a brain disorder that causes disabling involuntary muscle contractions and abnormal postures .", "When this is the only feature , it is termed isolated dystonia .", "The pathogenic molecular mechanisms underlying the neuronal dysfunction that leads to dystonia remain to be elucidated and ...	[ "Dystonia is characterized by involuntary muscle contractions .", "Its many forms are genetically , phenotypically and etiologically diverse and it is unknown whether their pathogenesis converges on shared pathways .", "Mutations in THAP1 [THAP ( Thanatos-associated protein ) domain containing , apoptosis assoc...	[ "Dystonia is a brain disorder that causes disabling involuntary muscle contractions and abnormal postures .", "Mutations in THAP1 , a zinc-finger transcription factor , cause DYT6 , but its neuronal targets and functions are unknown .", "In this study , we sought to determine the effects of Thap1C54Y and ΔExon2...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "fluorescence imaging", "amorphous solids", "medicine and health sciences", "methods and resources", "protein interactions", "glass", "endocrine physiology", "membrane proteins", "fluorophotometry", "materials science", "growth factors", "cellular structures and organelles", "epidermal growt...	Direct visualization of single-molecule membrane protein interactions in living cells	journal.pbio.2006660	null	[ [ "Membrane proteins play crucial roles in communication between intracellular and extracellular environments across cell membranes [1] .", "Malfunctioning of membrane proteins often results in myriad diseases [2] , which makes these proteins major therapeutic targets [3] .", "Despite their importance i...	[ "Interactions between membrane proteins are poorly understood despite their importance in cell signaling and drug development .", "Here , we present a co-immunoimmobilization assay ( Co-II ) enabling the direct observation of membrane protein interactions in single living cells that overcomes the limitations of c...	[ "Protein–protein interactions govern cellular processes .", "The majority of these physical interactions previously identified are strong/permanent interactions , which typically remain unbroken even after purification .", "The weak/transient interactions between proteins have been implicated in the control of ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "learning", "decision making", "social sciences", "neuroscience", "learning and memory", "simulation and modeling", "age groups", "optimization", "adults", "cognitive psychology", "mathematics", "cognition", "research and analysis methods", "behavior", "adolescents", "people and places...	The Computational Development of Reinforcement Learning during Adolescence	journal.pcbi.1004953	null	[ [ "Adolescence is defined as the period of life that starts with the biological changes of puberty and ends with the individual attainment of a stable , independent role in society[1] .", "During this period , significant changes in value-based decision-making are observed[2] .", "Adolescents are often ...	[ "Adolescence is a period of life characterised by changes in learning and decision-making .", "Learning and decision-making do not rely on a unitary system , but instead require the coordination of different cognitive processes that can be mathematically formalised as dissociable computational modules .", "Here...	[ "We employed a novel learning task to investigate how adolescents and adults learn from reward versus punishment , and to counterfactual feedback about decisions .", "Computational analyses revealed that adults and adolescents did not implement the same algorithm to solve the learning task .", "In contrast to a...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "model organisms", "genetics", "biology", "molecular cell biology" ]	Strabismus Promotes Recruitment and Degradation of Farnesylated Prickle in Drosophila melanogaster Planar Polarity Specification	journal.pgen.1003654	null	[ [ "The Prickle ( Pk ) protein is one of the “core” planar polarity proteins which are necessary to polarise cells in the plane of epithelia in Drosophila melanogaster and vertebrates [1]–[3] .", "For example , in the fly wing the core proteins ensure that the single trichome that emerges from each cell alwa...	[ "The core planar polarity proteins are required to specify the orientation of structures that are polarised in the plane of the epithelium .", "In the Drosophila melanogaster wing , the core proteins localise asymmetrically at either proximal or distal cell edges .", "Asymmetric localisation is thought to be bi...	[ "The core planar polarity proteins are responsible for polarising structures in the plane of epithelia .", "For example in the fly wing , the core proteins are required for cells to make hairs that point towards the distal end of the wing .", "The core proteins localise asymmetrically in wing cells , either at ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "host cells", "viral transmission and infection", "virology", "biology", "microbiology", "viral replication" ]	Productive Parvovirus B19 Infection of Primary Human Erythroid Progenitor Cells at Hypoxia Is Regulated by STAT5A and MEK Signaling but not HIFα	journal.ppat.1002088	null	[ [ "Human parvovirus B19 ( B19V ) is the only parvovirus so far confirmed to be pathogenic to humans [1] .", "Infection by this virus is the cause of the highly contagious “fifth disease” in children .", "It can also result in serious , and occasionally fatal , hematologic diseases in susceptible patient...	[ "Human parvovirus B19 ( B19V ) causes a variety of human diseases .", "Disease outcomes of bone marrow failure in patients with high turnover of red blood cells and immunocompromised conditions , and fetal hydrops in pregnant women are resulted from the targeting and destruction of specifically erythroid progenit...	[ "Human parvovirus B19 ( B19V ) is the etiological agent of fifth disease seen in children , aplastic crisis in sickle cell disease patients , chronic anemia in immunocompromised patients , and hydrops fetalis in pregnant women .", "After more than 35 years since its discovery , B19V was still unable to be propaga...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell biology", "evolutionary biology", "molecular biology", "genetics and genomics" ]	Indirect Effects of Ploidy Suggest X Chromosome Dose, Not the X:A Ratio, Signals Sex in Drosophila	journal.pbio.0050332	Sex is determined by X chromosome number rather than by the value of the X:autosome ratio in Drosophila.	[ [ "Animals distinguish between numbers or kinds of sex chromosomes both to determine sex and to compensate for unequal gene expression between heterogametic ( XY and ZW ) and homogametic ( XX and ZZ ) sexes .", "In Drosophila and Caenorhabditis elegans , sex and dosage compensation are linked through geneti...	[ "In the textbook view , the ratio of X chromosomes to autosome sets , X:A , is the primary signal specifying sexual fate in Drosophila .", "An alternative idea is that X chromosome number signals sex through the direct actions of several X-encoded signal element ( XSE ) proteins .", "In this alternative , the i...	[ "In the fruit fly , Drosophila , chromosomal signals determine sex .", "Diploid flies with two X chromosomes are female , whereas those with one X are male .", "Conventionally , it is thought that the ratio of the number of X chromosomes to autosomes ( X:A ) constitutes the signal , because triploid flies beari...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biophysics", "neurological disorders" ]	Structural Polymorphism of 441-Residue Tau at Single Residue Resolution	journal.pbio.1000034	Nuclear magnetic resonance spectroscopy reveals the conformations of Tau, the protein that plays a central role in the progression of Alzheimer disease.	[ [ "Tau protein was originally discovered as a neuronal microtubule-associated protein ( MAP ) that stabilizes microtubules ( MTs ) and supports the outgrowth of axons [1 , 2] .", "The protein can modulate the transport of vesicles and organelles along MTs , serves as an anchor for enzymes , and regulates th...	[ "Alzheimer disease is characterized by abnormal protein deposits in the brain , such as extracellular amyloid plaques and intracellular neurofibrillary tangles .", "The tangles are made of a protein called tau comprising 441 residues in its longest isoform .", "Tau belongs to the class of natively unfolded prot...	[ "The Tau protein , which plays a central role in the progression of Alzheimer disease , is normally expressed in nerve axons , where it stabilizes microtubules ( MTs ) , supports the outgrowth of axons , and modulates the transport of vesicles and organelles along MTs .", "In Alzheimer disease , Tau becomes exces...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "systems biology", "control engineering", "theoretical biology", "engineering and technology", "biology and life sciences", "computational biology", "neuroscience" ]	Optimal Schedules of Light Exposure for Rapidly Correcting Circadian Misalignment	journal.pcbi.1003523	null	[ [ "Modern society requires individuals to be awake and alert at times that conflict with their internal circadian ( ∼24-hour ) timekeeping systems .", "In year 2012 over 60 million Americans traveled overseas , subjecting themselves to long periods of circadian mistiming , impaired sleep , and low performan...	[ "Jet lag arises from a misalignment of circadian biological timing with the timing of human activity , and is caused by rapid transmeridian travel .", "Jet lag's symptoms , such as depressed cognitive alertness , also arise from work and social schedules misaligned with the timing of the circadian clock .", "Us...	[ "When our body's internal timekeeping system becomes misaligned with the time of day in the outside world , many negative effects can be felt , including decreased performance , improper sleep , and jet lag .", "When misalignment is prolonged , it can also lead to serious medical conditions , including cancer , c...	2014
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "computational biology/macromolecular structure analysis", "evolutionary biology/microbial evolution and genomics", "microbiology/medical microbiology", "biophysics/structural genomics", "biophysics/experimental biophysical methods", "microbiology/microbial evolution and genomics", "computational biolog...	Structure of the Head of the Bartonella Adhesin BadA	journal.ppat.1000119	null	[ [ "Adherence to the host is a key event in bacterial pathogenesis .", "The mediators of this process , called adhesins , form a heterogenous group that vary in architecture , domain content and mechanism of binding .", "Trimeric autotransporter adhesins , also referred to as OCAs for oligomeric coiled-c...	[ "Trimeric autotransporter adhesins ( TAAs ) are a major class of proteins by which pathogenic proteobacteria adhere to their hosts .", "Prominent examples include Yersinia YadA , Haemophilus Hia and Hsf , Moraxella UspA1 and A2 , and Neisseria NadA .", "TAAs also occur in symbiotic and environmental species and...	[ "The ability to adhere is an important aspect of the interaction between bacteria and their environment .", "Adhesion allows them to aggregate into colonies , form biofilms with other species , and colonize surfaces .", "Where the surfaces are provided by other organisms , adhesion can lead to a wide range of o...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Minor Type IV Collagen α5 Chain Promotes Cancer Progression through Discoidin Domain Receptor-1	journal.pgen.1005249	null	[ [ "Basement membranes ( BMs ) , specialized extracellular matrices separating epithelial and endothelial cells from underlying mesenchyme , provide cells with structural support , as well as morphogenic and functional cues [1–3] .", "Type IV collagens ( Col IV ) are major components of BMs [1 , 3] .", "...	[ "Type IV collagens ( Col IV ) , components of basement membrane , are essential in the maintenance of tissue integrity and proper function .", "Alteration of Col IV is related to developmental defects and diseases , including cancer .", "Col IV α chains form α1α1α2 , α3α4α5 and α5α5α6 protomers that further for...	[ "Collagens , the major extracellular matrix components in most vertebrate tissues , provide cells with structural and functional support .", "Collagens are trimers of collagen α chains .", "Multiple trimers are formed by highly homologous α chains for certain types of collagens ( e . g . α1α1α2 , α3α4α5 and α5α...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Lifespan Extension Conferred by Endoplasmic Reticulum Secretory Pathway Deficiency Requires Induction of the Unfolded Protein Response	journal.pgen.1004019	null	[ [ "Membrane and secretory proteins fold into their native conformations in the endoplasmic reticulum ( ER ) assisted by chaperones , thiol-disulfide oxidoreductases and other systems supporting protein post-translational control .", "Impairments in this complex process cause unfolded proteins to accumulate ...	[ "Cells respond to accumulation of misfolded proteins in the endoplasmic reticulum ( ER ) by activating the unfolded protein response ( UPR ) signaling pathway .", "The UPR restores ER homeostasis by degrading misfolded proteins , inhibiting translation , and increasing expression of chaperones that enhance ER pro...	[ "Impaired protein function caused by protein misfolding and aggregation has been implicated in the development of age-related diseases and regulation of lifespan .", "Accumulation of misfolded proteins in the endoplasmic reticulum , a cellular organelle responsible for protein folding and trafficking , activates ...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/bacterial infections", "infectious diseases/neglected tropical diseases", "infectious diseases/epidemiology and control of infectious diseases" ]	Estimating Household and Community Transmission of Ocular Chlamydia trachomatis	journal.pntd.0000401	null	[ [ "Trachoma is the leading cause of infectious blindness worldwide .", "Eight million people are visually impaired from the disease and a further 46 million people with active disease are in need of treatment to prevent blindness [1] .", "Mass drug administration ( MDA ) with antibiotics ( predominantly...	[ "Community-wide administration of antibiotics is one arm of a four-pronged strategy in the global initiative to eliminate blindness due to trachoma .", "The potential impact of more efficient , targeted treatment of infected households depends on the relative contribution of community and household transmission o...	[ "Trachoma is a major cause of blindness worldwide and results from ocular infection with the bacterium Chlamydia trachomatis .", "Mass distribution of antibiotics in communities is part of the strategy to eliminate blindness due to trachoma .", "Targeted treatment of infected households could be more efficient ...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular dynamics", "biophysics theory", "chemistry", "biology", "computational chemistry", "biophysics" ]	Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations	journal.pcbi.1003034	null	[ [ "The interplay between membrane lipids and proteins plays a key role in a number of cellular processes [1] , [2] including the replication and release of viruses .", "For example , in the latter stages of the replication cycle of influenza virus A , the viral genome and associated proteins gather at the p...	[ "The association of hemagglutinin ( HA ) with lipid rafts in the plasma membrane is an important feature of the assembly process of influenza virus A . Lipid rafts are thought to be small , fluctuating patches of membrane enriched in saturated phospholipids , sphingolipids , cholesterol and certain types of protein...	[ "The cell membrane is composed of a wide variety of lipids and proteins .", "Until recently , these were thought to be mixed evenly , but we now have evidence of the existence of “lipid rafts” — small , slow-moving areas of membrane in which certain types of lipid and protein accumulate .", "Rafts have many imp...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "toxins", "immune physiology", "pathology and laboratory medicine", "liquid chromatography", "immunology", "tropical diseases", "vertebrates", "animals", "toxicology", "toxic agents", "cobras", "reptiles", "neglected tropical diseases", "high performance l...	Analysis of the efficacy of Taiwanese freeze-dried neurotoxic antivenom against Naja kaouthia, Naja siamensis and Ophiophagus hannah through proteomics and animal model approaches	journal.pntd.0006138	null	[ [ "Envenomation through snakebite is an important public health issue in many regions of the world , particularly in tropical countries [1–3] .", "An estimated 421 , 000 to 1 , 841 , 000 envenomations and 20 , 000 to 94 , 000 deaths occur globally each year owing to snakebites .", "The regions of highes...	[ "In Southeast Asia , envenoming resulting from cobra snakebites is an important public health issue in many regions , and antivenom therapy is the standard treatment for the snakebite .", "Because these cobras share a close evolutionary history , the amino acid sequences of major venom components in different sna...	[ "Cobra envenomation is a public health issue in Southeast Asia .", "Currently , antivenom therapy is the standard treatment for snakebite .", "However , antivenoms are not available in many rural countries and communities or have only limited effectiveness .", "Taiwan has wealth of experience in producing ant...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology", "computational biology", "neuroscience" ]	A Dynamical Role for Acetylcholine in Synaptic Renormalization	journal.pcbi.1002939	null	[ [ "Sleep is crucial for normal cognitive function as evidenced by the many cognitive impairments associated with chronic sleep loss [1] , [2] .", "A leading proposal for the function of sleep , called the synaptic renormalization hypothesis , posits that sleep is required to maintain synaptic balance in the...	[ "Although sleep is a fundamental behavior observed in virtually all animal species , its functions remain unclear .", "One leading proposal , known as the synaptic renormalization hypothesis , suggests that sleep is necessary to counteract a global strengthening of synapses that occurs during wakefulness .", "E...	[ "The function of sleep is one of the greatest mysteries in contemporary neuroscience .", "Nearly every species of animal requires it , yet we do not know why .", "One idea , known as the synaptic renormalization hypothesis , suggests that waking results in a global increase in the strengths of connections in th...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "chagas disease", "epidemiology", "infectious disease epidemiology", "neglected tropical diseases", "parasitic diseases" ]	Prevalence of Trypanosoma cruzi Infection among People Aged 15 to 89 Years Inhabiting the Department of Casanare (Colombia)	journal.pntd.0002113	null	[ [ "Chagas disease is caused by the protozoan hemoflagellated Trypanosoma cruzi .", "The infection is transmitted to humans or many other vertebrates by insects of the Triatoma family , usually through the deposit of infecting forms of the parasite on the stool , near mucosae or minimal lesions in the skin [...	[ "The purpose of this study was to calculate the seroprevalence of Trypanosoma cruzi infection in a sample of inhabitants from a region considered to be at high risk of natural transmission of Chagas disease in Colombia .", "A cross-sectional study was conducted in subjects from 5 municipalities , recruited in urb...	[ "Chagas disease is caused by the chronic infection with the parasite Trypanosoma cruzi and is transmitted to human beings by bloodsucking insects of the Triatoma family .", "This condition is endemic in Central and South America , and is acquiring relevance in the rest of the world since it can also be transmitte...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "meiosis", "plant anatomy", "plant growth and development", "cell cycle and cell division", "plant embryo anatomy", "ovules", "cell processes", "brassica", "endosperm", "developmental biology", "plant science", "model organisms", "experimental organism systems", "embryos", "plants", "r...	Arabidopsis ICK/KRP cyclin-dependent kinase inhibitors function to ensure the formation of one megaspore mother cell and one functional megaspore per ovule	journal.pgen.1007230	null	[ [ "The cyclin-dependent kinase ( CDK ) inhibitors are proteins of usually small molecular masses able to inhibit CDKs through direct binding .", "Since CDKs are central to cell cycle regulation in eukaryotes , CDK inhibitors are important cell cycle regulators .", "The ICK/KRP family of plant CDK inhibi...	[ "In most plants , the female germline starts with the differentiation of one megaspore mother cell ( MMC ) in each ovule that produces four megaspores through meiosis , one of which survives to become the functional megaspore ( FM ) .", "The FM further develops into an embryo sac .", "Little is known regarding ...	[ "In most plants , the female germline starts with the differentiation of one megaspore mother cell ( MMC ) in each ovule that produces multiple megaspores through meiosis .", "One of the megaspores in a fixed position survives to become the functional megaspore ( FM ) while the other megaspores undergo degenerati...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology", "biology", "microbiology", "molecular cell biology" ]	Induction of Strain-Transcending Antibodies Against Group A PfEMP1 Surface Antigens from Virulent Malaria Parasites	journal.ppat.1002665	null	[ [ "The design of new drugs and vaccines against many infectious diseases is hindered by sequence diversity in key pathogen antigens [1] .", "This is a particular problem in the deadliest form of human malaria caused by P . falciparum , in which important targets of protective immunity are highly variable an...	[ "Sequence diversity in pathogen antigens is an obstacle to the development of interventions against many infectious diseases .", "In malaria caused by Plasmodium falciparum , the PfEMP1 family of variant surface antigens encoded by var genes are adhesion molecules that play a pivotal role in malaria pathogenesis ...	[ "Malaria remains one of the world's most deadly diseases .", "Life-threatening malaria is linked to a process called rosetting , in which malaria parasite-infected red blood cells bind to uninfected red cells to form aggregates that block blood flow in vital organs such as the brain .", "Current efforts to deve...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biotechnology", "medicine and health sciences", "luciferase", "engineering and technology", "enzymes", "immunology", "microbiology", "vertebrates", "enzymology", "animals", "plasmid construction", "oncology", "genome analysis", "dna construction", "molecular biology techniques", "gene...	Avian oncogenic herpesvirus antagonizes the cGAS-STING DNA-sensing pathway to mediate immune evasion	journal.ppat.1007999	null	[ [ "Herpesviruses are important pathogens associated with a wide range of diseases in humans and animals .", "In particular , Marek’s disease virus ( MDV ) constitutes a highly pathogenic and oncogenic herpesvirus of chickens [1] .", "As a disease that affects poultry worldwide with economic implications...	[ "The cellular DNA sensor cGMP-AMP synthase ( cGAS ) detects cytosolic viral DNA via the stimulator of interferon genes ( STING ) to initiate innate antiviral response .", "Herpesviruses are known to target key immune signaling pathways to persist in an immune-competent host .", "Marek’s disease virus ( MDV ) , ...	[ "Marek’s disease virus ( MDV ) is an avian oncogenic herpesvirus that causes a fatal disease in poultry worldwide .", "Chickens infected with MDV become more susceptible to secondary viral or bacterial infections .", "However , the mechanisms of MDV-induced immunosuppression and tumorigenesis remain largely unk...	2019
[ "Introduction", "Methods", "Results/Discussion" ]	[ "biochemistry", "computational chemistry", "molecular dynamics", "biochemistry simulations", "biophysic al simulations", "enzymes", "chemistry", "biology", "bioenergetics", "biophysics simulations", "biophysics", "computational biology" ]	Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase	journal.pcbi.1002674	null	[ [ "Bacterial denitrification is one of the examples of anaerobic respiration in which nitrate ( NO3− ) is stepwisely reduced to dinitrogen ( N2 ) [1]–[3] .", "During denitrification , the key intermediate step of the reduction of nitric oxide ( NO ) to nitrous oxide ( N2O ) is catalyzed by a membrane-bound ...	[ "Nitric oxide reductases ( NORs ) are membrane proteins that catalyze the reduction of nitric oxide ( NO ) to nitrous oxide ( N2O ) , which is a critical step of the nitrate respiration process in denitrifying bacteria .", "Using the recently determined first crystal structure of the cytochrome c-dependent NOR ( ...	[ "Denitrification is an anaerobic process performed by several bacteria as an alternative to aerobic respiration .", "A key intermediate step is catalyzed by the nitric oxide reductase ( NOR ) enzyme , which is situated in the cytoplasmic membrane .", "Proton delivery to the catalytic site inside NOR is an impor...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/cellular death and stress responses", "genetics and genomics/functional genomics", "cell biology/cell signaling", "immunology/immune response", "immunology/innate immunity" ]	A Quantitative RNAi Screen for JNK Modifiers Identifies Pvr as a Novel Regulator of Drosophila Immune Signaling	journal.ppat.1000655	null	[ [ "The adaptive immune response is a recent evolutionary acquisition by vertebrates .", "In contrast , the innate immune response is highly conserved among metazoans and is the first line of defense against invading pathogens [1] .", "Drosophila melanogaster is a powerful model for the study of innate i...	[ "Drosophila melanogaster responds to gram-negative bacterial challenges through the IMD pathway , a signal transduction cassette that is driven by the coordinated activities of JNK , NF-κB and caspase modules .", "While many modifiers of NF-κB activity were identified in cell culture and in vivo assays , the regu...	[ "Innate immunity is the sole immune response in the overwhelming majority of multicellular organisms and drives the sophisticated antigen-specific adaptive defenses of vertebrates .", "Defective regulation of immune signal transduction pathways has disastrous consequences for affected individuals and can result i...	2009
[ "Introduction", "Methods", "Results and discussion" ]	[ "larvicides", "invertebrates", "medicine and health sciences", "rna interference", "gene regulation", "animals", "developmental biology", "fungi", "model organisms", "pest control", "experimental organism systems", "epigenetics", "insect vectors", "research and analysis methods", "saccha...	Characterization of a yeast interfering RNA larvicide with a target site conserved in the synaptotagmin gene of multiple disease vector mosquitoes	journal.pntd.0007422	null	[ [ "Larviciding , the application of microbial or chemical agents to kill mosquito larvae in aquatic habitats , is a key component of integrated mosquito control and disease prevention strategies .", "Aedes mosquitoes , the primary vectors of dengue , Zika , yellow fever , and chikungunya viruses , lay eggs ...	[ "New mosquito control strategies are vitally needed to address established and emerging arthropod-borne infectious diseases .", "Here we describe the characterization of a yeast interfering RNA larvicide that was developed through the genetic engineering of Saccharomyces cerevisiae ( baker’s yeast ) to express a ...	[ "It is critical that we develop new strategies for the environmentally safe control of disease vector mosquitoes .", "In this study , baker’s yeast was genetically engineered to produce interfering RNA molecules corresponding to the mosquito synaptotagmin ( syt ) gene , but which do not match any genes in humans ...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience" ]	Distinct Mammalian Precursors Are Committed to Generate Neurons with Defined Dendritic Projection Patterns	journal.pbio.0050300	How do adult-born neurons connect into specific brain circuits? The authors show that distinct progenitors are committed to generate the same neuron type, but with different prespecified projection patterns.	[ [ "Dendrites are the major source of synaptic input for neurons .", "Thus , the specific computation that a neuron can accomplish is largely determined by the synaptic partners that contact its dendrites .", "In many regions of the central nervous system , including the cortex , spinal cord , retina , a...	[ "The mechanisms that regulate how dendrites target different neurons to establish connections with specific cell types remain largely unknown .", "In particular , the formation of cell-type–specific connectivity during postnatal neurogenesis could be either determined by the local environment of the mature neuron...	[ "The mammalian brain contains a large number of different classes of neurons that are connected in a specific manner .", "A long-standing question is how such stereotyped connections emerge during the assembly of the brain .", "Here , we investigated whether neonatal and adult brain stem cells give rise to neur...	2007
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary biology/microbial evolution and genomics", "infectious diseases/neglected tropical diseases", "molecular biology/molecular evolution", "public health and epidemiology/epidemiology", "public health and epidemiology/infectious diseases", "microbiology/parasitology", "infectious diseases/prot...	Genome-Scale Multilocus Microsatellite Typing of Trypanosoma cruzi Discrete Typing Unit I Reveals Phylogeographic Structure and Specific Genotypes Linked to Human Infection	journal.ppat.1000410	null	[ [ "T . cruzi , the etiological agent of Chagas disease , is a vector borne zoonosis and considered the most important parasitic infection in Latin America .", "In excess of 10 million people are thought to carry the parasite , with ten times that number at risk ( http://www . who . int ) .", "Consistent...	[ "Trypanosoma cruzi is the most important parasitic infection in Latin America and is also genetically highly diverse , with at least six discrete typing units ( DTUs ) reported: Tc I , IIa , IIb , IIc , IId , and IIe .", "However , the current six-genotype classification is likely to be a poor reflection of the t...	[ "The arrival of the Trypanosoma cruzi online genome now provides vital information for the study of Chagas disease .", "Using this resource , we identified and developed a genome-scale panel of rapidly evolving microsatellite markers that can be used to unravel the micro-epidemiology of this parasite .", "We th...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome expression analysis", "evolutionary ecology", "physiological ecology", "plant biology", "plant science", "plant ecology", "ecological economics", "biology", "systems biology", "physiogenomics", "ecology", "genomics", "evolutionary biology", "plant-environment interactions", "gene...	Genome-Wide Patterns of Arabidopsis Gene Expression in Nature	journal.pgen.1002662	null	[ [ "Organisms in the real world are continuously exposed to multiple environmental signals and must respond appropriately to dynamic , fluctuating conditions found in nature [1] .", "Dynamic environmental signals can differ spatially and temporally during an individual's life cycle with different degrees of ...	[ "Organisms in the wild are subject to multiple , fluctuating environmental factors , and it is in complex natural environments that genetic regulatory networks actually function and evolve .", "We assessed genome-wide gene expression patterns in the wild in two natural accessions of the model plant Arabidopsis th...	[ "Plants in the real world are continuously exposed to multiple environmental signals and must respond appropriately to the dynamic conditions found in nature .", "Environmental signals can fluctuate during an individual's life cycle with varying degrees of predictability , and complex natural environments are whe...	2012
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Follow-up of an Asymptomatic Chagas Disease Population of Children after Treatment with Nifurtimox (Lampit) in a Sylvatic Endemic Transmission Area of Colombia	journal.pntd.0003465	null	[ [ "Chagas disease affects approximately 8 million people worldwide , and nearly 28 million are at risk [1 , 2] .", "It is estimated that 436 , 000 ( 1% of the population ) individuals are infected in Colombia [3 , 4] .", "The etiologic agent is the parasite Trypanosoma cruzi , which is transmitted prima...	[ "Chagas disease is an anthropozoonosis caused by Trypanosoma cruzi .", "Two drugs are currently used for the etiological treatment of the disease: Nifurtimox ( Lampit ) and Benznidazole .", "This study presents a quasi-experimental trial ( non-control group ) of sixty-two patients who were treated for Chagas di...	[ "Chagas disease is currently treated with two drugs , Benznidazole ( BNZ ) and Nifurtimox ( NFX ) .", "The need to find the ideal diagnostic technique for post treatment evaluation still exists , due to the known flaws of the currently used techniques .", "We performed an evaluation of the safety and effectiven...	2015
[ "Introduction", "Models", "Results", "Discussion" ]	[ "evolutionary biology", "theoretical biology", "biology and life sciences" ]	The Evolution of Multivariate Maternal Effects	journal.pcbi.1003550	null	[ [ "Since selection often varies both over space and time [1]–[3] , evolutionary mechanisms that increase adaptation to changing environments are considered to be highly advantageous [4] , [5] .", "Conventional studies focus on mechanisms such as bet-hedging [6]–[8] and , in particular , within-generational ...	[ "There is a growing interest in predicting the social and ecological contexts that favor the evolution of maternal effects .", "Most predictions focus , however , on maternal effects that affect only a single character , whereas the evolution of maternal effects is poorly understood in the presence of suites of i...	[ "In numerous organisms , mothers influence the phenotype of their offspring by transmitting hormones , antibodies and nutrients to the embryo .", "Evolutionary studies that make predictions about the evolution of these maternal effects typically focus , however , on single maternal characters only , in isolation ...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "taxonomy", "horizontal gene transfer", "medicine and health sciences", "microbiology", "gene transfer", "antibiotic resistance", "phylogenetics", "data management", "phylogenetic analysis", "genome analysis", "dna recombination", "dna", "pharmacology", "microbial genetics", "homologous ...	Genetic exchanges are more frequent in bacteria encoding capsules	journal.pgen.1007862	null	[ [ "Extracellular capsules constitute the outermost layer of cells .", "They can be synthesized through different genetic pathways [1 , 2] and although some capsule types can be of proteic nature , notably the poly-γ-d-glutamate or PGA capsules produced by Bacillus anthracis [3] , the vast majority are high ...	[ "Capsules allow bacteria to colonize novel environments , to withstand numerous stresses , and to resist antibiotics .", "Yet , even though genetic exchanges with other cells should be adaptive under such circumstances , it has been suggested that capsules lower the rates of homologous recombination and horizonta...	[ "Previous works showed that bacteria encoding capsules are better colonizers and are dominant in most environments suggesting a positive role for capsules in the genetic diversification of bacteria .", "Yet , it has been repeatedly suggested , based almost exclusively studies in few model species , that such bact...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "action potentials", "engineering and technology", "nervous system", "membrane potential", "electrophysiology", "neuroscience", "physiological processes", "systems science", "mathematics", "prototypes", "computer and information sciences", "ergodicity", "dev...	Limited synapse overproduction can speed development but sometimes with long-term energy and discrimination penalties	journal.pcbi.1005750	null	[ [ "The phenomenon of net synapse overproduction in brain development is well-documented [1–4] but , as far as we can find , almost nothing definite is said about its purpose .", "Nevertheless , misregulation of this overproduction phenomenon is postulated to be a possible cause of autism [5–7] .", "The ...	[ "Neural circuit development requires that synapses be formed between appropriate neurons .", "In addition , for a hierarchical network , successful development involves a sequencing of developmental events .", "It has been suggested that one mechanism that helps speed up development of proper connections is an ...	[ "The brain processes information by building and adjusting neural connections , and as an organism learns about the environment , it incorporates associations between features of the environment into these adjustable connections .", "Organisms , however , are not born with these connections; synapses must develop...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Semen CD4+ T Cells and Macrophages Are Productively Infected at All Stages of SIV infection in Macaques	journal.ppat.1003810	null	[ [ "More than 33 million people are currently living with HIV/AIDS worldwide .", "Almost 80% of new infections occur through sexual intercourse .", "Semen is thus one of the major factors in HIV transmission .", "Most studies on HIV sexual transmission have focused on the role of cell-free particles ...	[ "The mucosal events of HIV transmission have been extensively studied , but the role of infected cells present in the genital and rectal secretions , and in the semen , in particular , remains a matter of debate .", "As a prerequisite to a thorough in vivo investigation of the early transmission events through in...	[ "Human Immunodeficiency Virus infection is predominantly transmitted by mucosal exposure , after sexual intercourse .", "Although substantial progresses have been recently achieved in our understanding of the mechanisms of HIV mucosal transmission , many questions remain .", "Semen is one of the major sources f...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "biology" ]	The Chromosomal Passenger Protein Birc5b Organizes Microfilaments and Germ Plasm in the Zebrafish Embryo	journal.pgen.1003448	null	[ [ "A fundamental feature of cell biology is cytoskeletal cross-talk between microtubule and microfilament networks .", "One key cellular process dependent on these interactions is the positioning of the contractile ring during cytokinesis .", "Two major groups of microtubules are involved in contractile...	[ "Microtubule-microfilament interactions are important for cytokinesis and subcellular localization of proteins and mRNAs .", "In the early zebrafish embryo , astral microtubule-microfilament interactions also facilitate a stereotypic segregation pattern of germ plasm ribonucleoparticles ( GP RNPs ) , which is cri...	[ "We address mechanisms by which germ cell precursors , a cell type that generates sperm and eggs for future generations , are specified in the zebrafish .", "Germ cell-specific genes are highly conserved across species , and in many animals germ cells are specified by the inheritance of germ plasm , a specialized...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "mast cells", "cell physiology", "medicine and health sciences", "neurochemistry", "toxins", "pathology and laboratory medicine", "chemical compounds", "immunology", "vertebrates", "neuroscience", "organic compounds", "animals", "toxic agents", "toxicology", "hormones", "signs and symp...	Neurogenic mediators contribute to local edema induced by Micrurus lemniscatus venom	journal.pntd.0005874	null	[ [ "Micrurus is one of the four snake genera of medical importance in Brazil .", "Coral snakes can be found from the southern United States to Argentina [1 , 2] .", "There are at least thirty species in Brazil , and these have a broad geographic distribution and inhabit a variety of habitats [3] .", ...	[ "Micrurus is one of the four snake genera of medical importance in Brazil .", "Coral snakes have a broad geographic distribution from the southern United States to Argentina .", "Micrurine envenomation is characterized by neurotoxic symptoms leading to dyspnea and death .", "Moreover , various local manifesta...	[ "Micrurus venoms have neurotoxic activity that is responsible for the serious sequelae in human envenomation .", "However , various local manifestations of envenoming have been described in patients bitten by different Micrurus species and edematogenic activity has been experimentally demonstrated .", "Despite ...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "cell walls", "plant anatomy", "microtubules", "plant growth and development", "plant cell biology", "plant embryo anatomy", "organisms", "plant cell walls", "developmental biology", "plant science", "seedlings", "plants", "morphogenesis", "cellular structures and organelles", "pattern f...	A Theoretical Model of Jigsaw-Puzzle Pattern Formation by Plant Leaf Epidermal Cells	journal.pcbi.1004833	null	[ [ "Throughout growth and differentiation , plant cells display various shapes that are primarily determined by the cell wall [1 , 2] .", "Leaf epidermal cells in dicotyledonous plants have jigsaw puzzle–like shapes with winding cell wall [3 , 4] .", "Prior to leaf expansion , epidermal cells have a simp...	[ "Plant leaf epidermal cells exhibit a jigsaw puzzle–like pattern that is generated by interdigitation of the cell wall during leaf development .", "The contribution of two ROP GTPases , ROP2 and ROP6 , to the cytoskeletal dynamics that regulate epidermal cell wall interdigitation has already been examined; howeve...	[ "It is well known that plant epidermal cells show beautiful jigsaw-puzzle like pattern .", "However , mechanism of this pattern formation is not well understood .", "In this study , we integrated known experimental information and mathematical modeling to reproduce the main features of the pattern formation—mai...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/cellular microbiology and pathogenesis", "immunology/immune response", "virology/animal models of infection", "immunology/innate immunity", "virology/emerging viral diseases", "immunology/genetics of the immune system", "virology/mechanisms of resistance and susceptibility, including host ge...	MyD88 Is Required for Protection from Lethal Infection with a Mouse-Adapted SARS-CoV	journal.ppat.1000240	null	[ [ "In 2003 , a novel coronavirus , SARS-CoV , emerged from zoonotic pools of virus in China to cause a global outbreak of Severe and Acute Respiratory Syndrome ( SARS ) affecting 29 countries , causing over 8000 human cases and greater than 700 deaths [1]–[3] .", "The clinical course of SARS-CoV disease in ...	[ "A novel human coronavirus , SARS-CoV , emerged suddenly in 2003 , causing approximately 8000 human cases and more than 700 deaths worldwide .", "Since most animal models fail to faithfully recapitulate the clinical course of SARS-CoV in humans , the virus and host factors that mediate disease pathogenesis remain...	[ "In 2002 , a new human coronavirus ( CoV ) , termed SARS-CoV , emerged in southern China from coronaviruses circulating within live animals sold for food .", "Due to the ease and speed of human global travel , this new respiratory virus rapidly spread worldwide , illustrating the need to better understand how the...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biotechnology", "plant science", "plant genomics", "biology and life sciences", "plant biotechnology" ]	Genome-Wide Nucleosome Positioning Is Orchestrated by Genomic Regions Associated with DNase I Hypersensitivity in Rice	journal.pgen.1004378	null	[ [ "The fundamental unit of chromatin is the nucleosome , which consists of 147 bp of DNA wrapped around a histone octamer containing four core histones ( H3 , H4 , H2A , and H2B ) [1] .", "Since the DNA has to bend sharply around the surface of the histone octamer , flexible or intrinsically curved sequence...	[ "Nucleosome positioning dictates the DNA accessibility for regulatory proteins , and thus is critical for gene expression and regulation .", "It has been well documented that only a subset of nucleosomes are reproducibly positioned in eukaryotic genomes .", "The most prominent example of phased nucleosomes is t...	[ "The fundamental unit of chromatin is the nucleosome , which consists of 147 bp of DNA wrapped around a histone octamer containing four core histones ( H3 , H4 , H2A , and H2B ) .", "Nucleosome positioning in the genome affects the DNA accessibility for regulatory proteins , and thus is critical for gene expressi...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious diseases/viral infections", "public health and epidemiology/infectious diseases", "infectious diseases/epidemiology and control of infectious diseases" ]	Relationship between Transmission Intensity and Incidence of Dengue Hemorrhagic Fever in Thailand	journal.pntd.0000263	null	[ [ "Dengue is the most prevalent vector-borne viral disease , the distribution of which has been expanding continually [1] .", "Dengue virus is transmitted by Aedes mosquitoes [2]–[4] , which breed predominantly in water-holding containers within human habitats .", "Infections with dengue virus may manif...	[ "Dengue is the most prevalent mosquito-borne virus , and potentially fatal dengue hemorrhagic fever ( DHF ) occurs mainly in secondary infections .", "It recently was hypothesized that , due to the presence of cross-immunity , the relationship between the incidence of DHF and transmission intensity may be negativ...	[ "An infection with dengue virus may lead to dengue hemorrhagic fever ( DHF ) , a dangerous illness .", "There is no approved vaccine for this most prevalent mosquito-borne virus , which infects tens of millions ( or more ) people annually .", "Therefore , health authorities have been putting an emphasis on redu...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "sequencing techniques", "pseudogenes", "population genetics", "genomic databases", "platinum", "genome analysis", "gene types", "molecular biology techniques", "population biology", "research and analysis methods", "sequence analysis", "genome complexity", "sequence alignment", "chromosom...	Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads	journal.pcbi.1005117	null	[ [ "The variation between human genomes in gene copy number is understudied and poorly characterized .", "One such region where this variation is known to exist is the immunoglobulin heavy variable ( IGHV ) locus .", "It is a vital component of the adaptive immune system , containing the V genes that cod...	[ "The study of genomic regions that contain gene copies and structural variation is a major challenge in modern genomics .", "Unlike variation involving single nucleotide changes , data on the variation of copy number is difficult to collect and few tools exist for analyzing the variation between individuals .", ...	[ "Regions of the human genome that vary in gene copy number are challenging to identify and analyze .", "This is particularly true for the immunoglobulin heavy variable locus ( IGHV ) , which codes for a component of the antibody molecule .", "Previous approaches to interrogate the IGHV locus using locus-specifi...	2016
[ "Introduction", "Results", "Discussion" ]	[ "cognitive science", "medicine and health sciences", "rna interference", "chemical compounds", "disaccharides", "nervous system", "carbohydrates", "neuroscience", "organic compounds", "learning and memory", "cognition", "memory", "epigenetics", "long term memory", "lipids", "genetic in...	Antimicrobial peptides modulate long-term memory	journal.pgen.1007440	null	[ [ "In most animals modifying behavior based on past experiences is important for survival and reproductive success[1] .", "To achieve these experience-dependent behavioral modifications , organisms must form memories of specific situations and maintain them to guide future behavior .", "Given that anima...	[ "Antimicrobial peptides act as a host defense mechanism and regulate the commensal microbiome .", "To obtain a comprehensive view of genes contributing to long-term memory we performed mRNA sequencing from single Drosophila heads following behavioral training that produces long-lasting memory .", "Surprisingly ...	[ "It is becoming evident that the nervous system and immune system share not only some of the same molecular logic but also the same components .", "Here , we report a novel and unanticipated example of how immune genes influence nervous system function .", "Exploring how Drosophila form long-lasting memories of...	2018
[ "Introduction", "Model", "Discussion" ]	[ "antimicrobials", "cell death", "medicine and health sciences", "viral transmission and infection", "antiviral therapy", "drugs", "cell processes", "immunology", "microbiology", "viral structure", "preventive medicine", "developmental biology", "pharmaceutics", "pharmacology", "vaccinati...	Life cycle synchronization is a viral drug resistance mechanism	journal.pcbi.1005947	null	[ [ "Viral infections are a major cause of human morbidity and mortality [1] .", "While vaccines to prevent viral illnesses have existed for over a century , it is only in the past several decades that drugs directly targeting viral replication have been developed .", "Antiviral drugs now exist for pathog...	[ "Viral infections are one of the major causes of death worldwide , with HIV infection alone resulting in over 1 . 2 million casualties per year .", "Antiviral drugs are now being administered for a variety of viral infections , including HIV , hepatitis B and C , and influenza .", "These therapies target a spec...	[ "Viral infections such as HIV , hepatitis B , hepatitis C , and influenza may be treated with antiviral drug therapy .", "These drugs generally block a specific phase of the virus’s life cycle , preventing it from replicating in the body .", "Often , a virus population can evolve drug resistance by acquiring mu...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	Cell-Autonomous Gβ Signaling Defines Neuron-Specific Steady State Serotonin Synthesis in Caenorhabditis elegans	journal.pgen.1005540	null	[ [ "Serotonin ( 5-HT ) is a neuromodulator implicated in stress-triggered behaviors such as aggression , anxiety , as well as in diverse innate behaviors and physiological processes ranging from food intake to rhythmic motor acts and circadian cycles [1] .", "Increasing evidence suggests that too much or too...	[ "Heterotrimeric G proteins regulate a vast array of cellular functions via specific intracellular effectors .", "Accumulating pharmacological and biochemical studies implicate Gβ subunits as signaling molecules interacting directly with a wide range of effectors to modulate downstream cellular responses , in addi...	[ "Levels of neurotransmitter serotonin synthesis shape disparate behaviors in evolutionary diverse organisms , but the mechanisms defining steady state serotonin synthesis in functionally distinct neuronal types remain unknown .", "A genetic screen for neuron-specific serotonin synthesis mutants in Caenorhabditis ...	2015
[ "Introduction", "Material & methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "education", "mycetoma", "interpersonal relationships", "sociology", "tropical diseases", "social sciences", "health care", "signs and symptoms", "neglected tropical diseases", "fungal diseases", "patients", "infectious d...	The disabling consequences of Mycetoma	journal.pntd.0007019	null	[ [ "Mycetoma is a neglected tropical disease frequently affecting the poorest of the poor in remote , poor communities [1] .", "It is endemic in many tropical and subtropical countries around the world including Sudan [2 , 3] .", "The geographical distribution of mycetoma depends on a range of environmen...	[ "Mycetoma is a neglected tropical disease endemic in tropical and subtropical countries , particularly Sudan .", "The disease is characterised by the triad of painless subcutaneous mass , multiple sinuses and discharge that contain grains .", "It is a chronic , debilitating disease most commonly affecting the f...	[ "Mycetoma is a neglected tropical disease endemic in many tropical and subtropical countries affecting poor , rural populations .", "It commonly affects the feet or hands and leads to substantial chronic morbidity , loss of function and disability .", "The disabling consequences of mycetoma have not been studie...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "biochemistry" ]	NleG Type 3 Effectors from Enterohaemorrhagic Escherichia coli Are U-Box E3 Ubiquitin Ligases	journal.ppat.1000960	null	[ [ "One of the best-studied molecular machineries in bacteria-host cell interactions is the Type 3 Secretion System ( T3SS ) .", "The T3SS is a syringe-like multi-protein complex spanning both the inner and outer bacterial membranes and the host cell membrane .", "It allows various Gram-negative bacteria...	[ "NleG homologues constitute the largest family of type 3 effectors delivered by pathogenic E . coli , with fourteen members in the enterohaemorrhagic ( EHEC ) O157:H7 strain alone .", "Identified recently as part of the non-LEE-encoded ( Nle ) effector set , this family remained uncharacterised and shared no sequ...	[ "Many bacterial pathogens utilize a multiprotein ‘‘injection needle’’ termed the type III secretion system to deliver a set of proteins called effectors into the host cell .", "These effectors then manipulate host signalling pathways to the advantage of the pathogen , often mimicking eukaryote-specific activities...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Loss and Gain of Natural Killer Cell Receptor Function in an African Hunter-Gatherer Population	journal.pgen.1005439	null	[ [ "Natural killer ( NK ) cells are versatile lymphocytes that contribute to reproduction and immune defense [1 , 2] .", "Modulating the activities of human NK-cells are the killer-cell immunoglobulin-like receptors ( KIR ) .", "These receptors engage the HLA class I ligands ( HLA-A , -B and -C ) express...	[ "Modulating natural killer cell functions in human immunity and reproduction are diverse interactions between the killer cell immunoglobulin-like receptors ( KIR ) of Natural Killer ( NK ) cells and HLA class I ligands on the surface of tissue cells .", "Dominant interactions are between KIR2DL1 and the C2 epitop...	[ "The genes that control the response of the human immune system vary enormously between individuals .", "Understanding the evolution of these genetic differences and how they individualize immune responses is central to understanding how the immune system works in health and disease .", "In this regard , the Kh...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa	journal.pntd.0003631	null	[ [ "Viral discovery is rapidly advancing , driven by the advent of high-throughput technologies like next-generation sequencing ( NGS ) [1] .", "Applying NGS as a diagnostic tool holds the promise for vastly expanding our understanding of the spectrum of microbes infecting humans , as it does not require a p...	[ "Next-generation sequencing ( NGS ) has the potential to transform the discovery of viruses causing unexplained acute febrile illness ( UAFI ) because it does not depend on culturing the pathogen or a priori knowledge of the pathogen’s nucleic acid sequence .", "More generally , it has the potential to elucidate ...	[ "Next-generation sequencing , a high-throughput method for sequencing DNA and RNA , has the potential to transform virus discovery because it does not depend on culturing the pathogen or a priori knowledge of the pathogen’s nucleic acid sequence .", "We used next-generation sequencing to identify RNA viruses pres...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "viral vaccines", "immunology", "microbiology", "animal models", "immunodeficiency viruses", "model organisms", "animal models of infection", "infectious diseases", "hiv", "biology", "macaque", "immunity", "virology", "viral diseases" ]	Cytotoxic Capacity of SIV-Specific CD8+ T Cells against Primary Autologous Targets Correlates with Immune Control in SIV-Infected Rhesus Macaques	journal.ppat.1003195	null	[ [ "Clues regarding the features of an effective cellular immune response capable of controlling a chronic lentiviral infection have come from humans who naturally restrict HIV replication referred to as long-term nonprogressors/elite controllers ( LTNP/EC ) [1]–[4] .", "LTNP/EC show an enrichment of some MH...	[ "Although the study of non-human primates has resulted in important advances for understanding HIV-specific immunity , a clear correlate of immune control over simian immunodeficiency virus ( SIV ) replication has not been found to date .", "In this study , CD8+ T-cell cytotoxic capacity was examined to determine...	[ "Clues regarding the features of effective immunity against lentiviruses have come from the study of non-human primates .", "We evaluated rhesus macaques infected with Simian Immunodeficiency Virus ( SIV ) , a lentivirus closely related to Human Immunodeficiency Virus ( HIV ) .", "In contrast to most SIV-infect...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "sequencing techniques", "dosage compensation", "invertebrates", "gene regulation", "dna clamps", "dna-binding proteins", "animals", "invertebrate genomics", "animal models", "drosophila melanogaster", "model organisms", "sequence motif analysis", "molecular biology techniques", "dna", "...	Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation	journal.pgen.1006120	null	[ [ "Changes in primary DNA sequence that occur over evolutionary time alter transcription factor occupancy on DNA [1 , 2] .", "Differential occupancy of transcription factors throughout the genome controls the essential gene regulatory programs that define growth and development [3] .", "Sex chromosome d...	[ "Dosage compensation is an essential process that equalizes transcript levels of X-linked genes between sexes by forming a domain of coordinated gene expression .", "Throughout the evolution of Diptera , many different X-chromosomes acquired the ability to be dosage compensated .", "Once each newly evolved X-ch...	[ "From stem cells to neurons , regulation of gene dosage is essential in all tissues and species in which it has been studied .", "Gene dosage must be balanced largely because it is critical to maintain the stoichiometry of components of multi-protein complexes that are encoded at diverse locations throughout the ...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma mansoni", "medicine and health sciences", "swimming", "body fluids", "helminths", "liquid chromatography", "tropical diseases", "parasitic diseases", "animals", "biological locomotion", "parasitology", "developmental biology", "gastropods", ...	A Biomphalaria glabrata peptide that stimulates significant behaviour modifications in aquatic free-living Schistosoma mansoni miracidia	journal.pntd.0006948	null	[ [ "Worldwide , an estimated 200 million people are infected and over 800 million people are at risk of infection of Schistosomiasis [1–3] , while over 200 , 000 people yearly will die from schistosomiasis-related illness [4] .", "This disease also has a high morbidity rate , being responsible for the loss o...	[ "The human disease schistosomiasis ( or bilharzia ) is caused by the helminth blood fluke parasite Schistosoma mansoni , which requires an intermediate host , the freshwater gastropod snail Biomphalaria glabrata ( the most common intermediate host ) .", "The free-swimming parasite miracidia utilise an excellent c...	[ "In aquatic environments , where the vast majority of animals live in darkness , key relationships are often formed and maintained by chemical communication ( including smell and taste ) .", "Parasites with an aquatic life phase rely on an exquisite sense of chemosensation to detect host biomolecules ( kairomones...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	The LUX Score: A Metric for Lipidome Homology	journal.pcbi.1004511	null	[ [ "A lipidome can be an indicator of health , disease , stress or metabolic state .", "Using model organisms , the role of lipid metabolism has been studied in diseases such as diabetes , metabolic syndrome , neurodegeneration and cancer [1–5] .", "To this end , lipidomes from yeast and fruit fly have b...	[ "A lipidome is the set of lipids in a given organism , cell or cell compartment and this set reflects the organism’s synthetic pathways and interactions with its environment .", "Recently , lipidomes of biological model organisms and cell lines were published and the number of functional studies of lipids is incr...	[ "Because of their role in health and disease , lipids are often the focus of biochemical studies .", "Advances in analytical biochemistry have made it possible to detect all the lipids from a cell , tissue or organism ( termed lipidome ) .", "Much of this research is based on model organisms , but it is difficu...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "typhus", "medicine and health sciences", "respiratory infections", "pathology and laboratory medicine", "drugs", "geographical locations", "microbiology", "australia", "pulmonology", "health care", "bacterial diseases", "signs and symptoms", "antibiotics", "pharmacolog...	The epidemiology and clinical features of rickettsial diseases in North Queensland, Australia: Implications for patient identification and management	journal.pntd.0007583	null	[ [ "Rickettsial infections are a common cause of hospitalization in tropical settings [1–4] , although early , definitive diagnosis is challenging in the rural locations where these infections are usually seen [5] .", "Antibiotic therapy is highly effective if started early in the disease course [6 , 7] , al...	[ "Rickettsial infections are a common cause of hospitalization in tropical settings , although early diagnosis is challenging in the rural locations where these infections are usually seen .", "This retrospective , clinical audit of microbiologically-confirmed cases of scrub typhus or spotted fever group ( SFG ) r...	[ "Rickettsial infections are a common cause of hospitalization in tropical settings , although early , definitive diagnosis is challenging in the rural and remote locations where they are usually seen .", "It is important to recognise rickettsial infections early in their disease course as they can lead to life-th...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "emulsions", "medicine and health sciences", "vitamin d deficiency", "chemical compounds", "drugs", "microbiology", "diet", "colloids", "antifungals", "organic compounds", "protein expression", "nutrition", "materials science", "pharmacology", "molecular biology techn...	Vitamin D deficiency is a potential risk factor for lipid Amphotericin B nephrotoxicity	journal.pntd.0007567	null	[ [ "Amphotericin B ( AmB ) is a macrolide polyene antibiotic frequently used for the treatment of invasive fungal infections ( IFI ) based on its broad-spectrum antifungal activity [1 , 2] .", "Despite its effectiveness in clinical trials , conventional AmB use is hampered by several adverse reactions and si...	[ "Invasive fungal infections ( IFI ) is a worldwide serious health problem and Amphotericin B ( AmB ) has been considered the drug of choice for IFI treatment .", "Despite its efficacy , clinical use of AmB has been associated with renal toxicity .", "Some lines of evidence have shown that an extemporaneous lipi...	[ "Amphotericin B ( AmB ) is the treatment of choice for systemic fungal infections .", "Despite its efficacy , clinical use of AmB has been associated with renal toxicity .", "In an attempt to improve the therapeutic effect and to reduce adverse reactions , lipid formulations of AmB were developed .", "Among t...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/microbial evolution and genomics", "evolutionary biology/evolutionary ecology", "computational biology/evolutionary modeling", "biochemistry/theory and simulation", "computational biology/systems biology" ]	A Mixture of “Cheats” and “Co-Operators” Can Enable Maximal Group Benefit	journal.pbio.1000486	It is commonly assumed that the world would be best off if everyone co-operates. Experimental and mathematical analysis of “co-operation” in yeast show why this isn't always the case.	[ [ "Wild caught strains of yeast are polymorphic [1] for the ability to produce the enzyme invertase .", "Strains with SUC2 secrete the enzyme , which catalyses the hydrolysis of sucrose into glucose and fructose .", "These are transported into the cell by hexose transporters and metabolized through glyc...	[ "Is a group best off if everyone co-operates ?", "Theory often considers this to be so ( e . g . the “conspiracy of doves” ) , this understanding underpinning social and economic policy .", "We observe , however , that after competition between “cheat” and “co-operator” strains of yeast , population fitness is ...	[ "The world is best off , it is usually presumed , when everyone co-operates .", "However , we discovered in a laboratory experiment involving yeasts that a population can grow more and faster when there is a mix of “cheats” and “co-operators . ”", "In this case “co-operator” cells produce a protein ( invertase ...	2010
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "condensation", "molecular dynamics", "chromosome structure and function", "condensed matter physics", "materials science", "forms of dna", "epigenetics", "dna", "macromolecules", "chromatin", "materials by structure", "polymers", "polymer chemistry", "chromosome biology", "proteins", ...	Modeling the functions of condensin in chromosome shaping and segregation	journal.pcbi.1006152	null	[ [ "The assembly of rod-shaped chromosomes is one of the most dramatic events occurring during the eukaryotic cell cycle .", "Upon entry into mitosis , the mass of chromatin distributed within the interphase nucleus is converted into a discrete set of rod-shaped chromosomes .", "This process , commonly r...	[ "The mechanistic details underlying the assembly of rod-shaped chromosomes during mitosis and how they segregate from each other to act as individually mobile units remain largely unknown .", "Here , we construct a coarse-grained physical model of chromosomal DNA and condensins , a class of large protein complexe...	[ "Immediately before a cell divides , chromosomal DNA in a eukaryotic cell is packaged into a discrete set of rod-shaped chromosomes .", "This process , known as mitotic chromosome assembly or condensation , secures the faithful segregation of genetic information into daughter cells .", "Central to this mechanis...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "skin infections", "virology", "immunology", "biology", "microbiology" ]	CD11b+, Ly6G+ Cells Produce Type I Interferon and Exhibit Tissue Protective Properties Following Peripheral Virus Infection	journal.ppat.1002374	null	[ [ "Typically , the acute innate immune response to a peripheral challenge involves rapid infiltration of Ly6C+Ly6G+ neutrophils , followed by Ly6C+Ly6G- monocytes , in a process that involves chemoattraction mediated by arachidonic acid metabolites , cytokines , and chemokines [1] .", "Both neutrophils and ...	[ "The goal of the innate immune system is containment of a pathogen at the site of infection prior to the initiation of an effective adaptive immune response .", "However , effector mechanisms must be kept in check to combat the pathogen while simultaneously limiting undesirable destruction of tissue resulting fro...	[ "During a natural virus infection , small doses of infectious virus are deposited at a peripheral infection site , and then a “race” ensues , in which the replicating virus attempts to “outpace” the responding immune system of the host .", "In the early phases of infection , the innate immune system must contain ...	2011
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genome expression analysis", "functional genomics", "genome evolution", "plant biology", "microbiology", "host-pathogen interaction", "genome sequencing", "plant science", "model organisms", "microbial evolution", "plant pathology", "arabidopsis thaliana", "plant microbiology", "proteins"...	Gene Gain and Loss during Evolution of Obligate Parasitism in the White Rust Pathogen of Arabidopsis thaliana	journal.pbio.1001094	null	[ [ "For more than 150 years , attempts to culture downy mildews , powdery mildews , and rusts on artificial nutrient media have been unsuccessful .", "The terms obligate parasitism and obligate biotrophy are used to denote organisms that live in such an obligatory association with living hosts [1] , [2] .", ...	[ "Biotrophic eukaryotic plant pathogens require a living host for their growth and form an intimate haustorial interface with parasitized cells .", "Evolution to biotrophy occurred independently in fungal rusts and powdery mildews , and in oomycete white rusts and downy mildews .", "Biotroph evolution and molecu...	[ "Plant pathogens that cannot grow except on their hosts are called obligate biotrophs .", "How such biotrophy evolves is poorly understood .", "In this study , we sequenced the genome of the obligate biotroph white rust pathogen ( Albugo laibachii , Oomycota ) of Arabidopsis .", "From comparisons with other o...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "molecular biology/transcription initiation and activation", "genetics and genomics/gene expression", "genetics and genomics/genome projects", "infectious diseases/helminth infections", "molecular biology/bioinformatics", "public health and epidemiology/global health", "public health and epidemiology/in...	A Reverse Transcriptase-PCR Assay for Detecting Filarial Infective Larvae in Mosquitoes	journal.pntd.0000251	null	[ [ "Lymphatic filariasis ( LF ) is a disabling tropical disease that is caused by filarial nematode parasites that are transmitted by mosquitoes .", "Brugia malayi and B . timori account for approximately 10% of the global LF burden of 120 million infected individuals [1] .", "The Global Programme to Eli...	[ "Existing molecular assays for filarial parasite DNA in mosquitoes cannot distinguish between infected mosquitoes that contain any stage of the parasite and infective mosquitoes that harbor third stage larvae ( L3 ) capable of establishing new infections in humans .", "We now report development of a molecular L3-...	[ "The Global Programme for the Elimination of Lymphatic Filariasis ( GPELF ) was launched in the year 1998 with the goal of eliminating lymphatic filariasis by 2020 .", "As the success of mass drug administration ( MDA ) in the global program drives the rates of infection in endemic populations to very low levels ...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "meiosis", "cell biology", "chromosome biology", "biology", "molecular cell biology" ]	Chromosome Painting Reveals Asynaptic Full Alignment of Homologs and HIM-8–Dependent Remodeling of X Chromosome Territories during Caenorhabditis elegans Meiosis	journal.pgen.1002231	null	[ [ "The success of sexual reproduction relies on the ability of diploid germ cells to generate haploid gametes through the specialized cell division program of meiosis .", "Haploidization relies on the faithful segregation of chromosomes from their homologous partners , which in turn relies on an ability to ...	[ "During early meiotic prophase , a nucleus-wide reorganization leads to sorting of chromosomes into homologous pairs and to establishing associations between homologous chromosomes along their entire lengths .", "Here , we investigate global features of chromosome organization during this process , using a chromo...	[ "Successful sexual reproduction relies on the ability of germ cells to faithfully segregate homologous chromosomes in meiosis , which requires accurate sorting of chromosomes into homologous pairs and alignment of homologs along their entire lengths .", "The mechanisms underlying homolog sorting and alignment are...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "inflammatory diseases", "medicine and health sciences", "body fluids", "leptospira", "pathology and laboratory medicine", "pathogens", "drugs", "tropical diseases", "geographical locations", "microbiology", "bacterial diseases", "antibiotics", "neglected tropical disease...	Prospective evaluation of accuracy and clinical utility of the Dual Path Platform (DPP) assay for the point-of-care diagnosis of leptospirosis in hospitalized patients	journal.pntd.0006285	null	[ [ "Leptospirosis is an important global cause of acute fever and a leading cause of morbidity among zoonotic diseases [1] .", "Annually , more than 1 million cases and 50 , 000 deaths occur worldwide [2] , and disease burden is estimated at 2 . 9 million disability adjusted life years ( DALYs ) [3] .", ...	[ "Early detection of leptospirosis with field-ready diagnostics may improve clinical management and mitigate outbreaks .", "We previously validated the point-of-care Dual Path Platform ( DPP ) for leptospirosis with sera in the laboratory .", "This prospective study compares the diagnostic accuracy and clinical ...	[ "The reliable , portable , point-of-care DPP assay effectively discriminates case status for patients presenting to hospital with acute febrile syndromes consistent with classic leptospirosis .", "Diagnostic accuracy of the finger stick DPP using the initial acute-phase specimen at the bedside is similar to serum...	2018
[ "Introduction", "Results", "Discussion", "Method" ]	[ "neuroscience/motor systems", "computational biology/computational neuroscience", "neuroscience" ]	Emergence of Functional Hierarchy in a Multiple Timescale Neural Network Model: A Humanoid Robot Experiment	journal.pcbi.1000220	null	[ [ "Functional hierarchy , defined broadly as the principle that complex entities may be", "segmented into simpler elements and that simple elements may be integrated into a", "complex entity , is a ubiquitous feature of information processing in biological", "neural systems [1]–[4] .", "For exam...	[ "It is generally thought that skilled behavior in human beings results from a", "functional hierarchy of the motor control system , within which reusable motor", "primitives are flexibly integrated into various sensori-motor sequence patterns .", "The underlying neural mechanisms governing the way in which co...	[ "Functional hierarchy in neural systems , defined as the principle that complex", "entities may be segmented into simpler elements and that simple elements may be", "integrated into a complex entity , is a challenging area of study in", "neuroscience .", "Such a functional hierarchy may be thought of intuit...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biology and life sciences", "medicine and health sciences" ]	IL28B Gene Polymorphism SNP rs8099917 Genotype GG Is Associated with HTLV-1-Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP) in HTLV-1 Carriers	journal.pntd.0003199	null	[ [ "Human T-cell lymphotropic Virus Type 1 ( HTLV-1 ) is a retrovirus etiologically linked to adult T-cell leukemia/lymphoma [1] , HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) and other inflammatory diseases [2] .", "This virus is endemic in Japan , Caribbean Basin , and some countri...	[ "The polymorphisms of IL28B have been described as important in the pathogenesis of infections caused by some viruses .", "The aim of this research was to evaluate whether IL28B gene polymorphisms ( SNP rs8099917 and SNP rs12979860 ) are associated with HAM/TSP .", "The study included 229 subjects , classified ...	[ "New evidence has shown that the pathogenic mechanism of disease-associated HTLV-1 infection is an impairment of the immunity .", "More recently , it has been demonstrated that IL28B polymorphisms are more likely to occur among HTLV-1 infected subjects and are associated with higher proviral loads in HTLV-1 carri...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "segmentation", "gene regulation", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "molecular genetics", "body plan organization", "morphogenesis", "biophysics simulations", "pattern formation", "regulatory networks", "biology", "biophysics", "phys...	Mutual Repression Enhances the Steepness and Precision of Gene Expression Boundaries	journal.pcbi.1002654	null	[ [ "The development of multicellular organisms requires spatially controlled cell differentiation .", "The positional information for the differentiating cells is typically provided by spatial concentration gradients of morphogen proteins .", "In the classical picture of morphogen-directed patterning , c...	[ "Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo .", "While gene expression is often highly erratic , embryonic development is usually exceedingly precise .", "In particular , gene expression boundaries are robust not only against intra-e...	[ "Embryonic development is controlled by spatial patterns of gene expression that seal the fate of each cell in the embryo .", "However , while development is typically very precise , gene expression is often very noisy .", "Indeed , a key question in current biology is how embryonic development can be so precis...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biology and life sciences", "medicine and health sciences" ]	Leishmania donovani Infection Causes Distinct Epigenetic DNA Methylation Changes in Host Macrophages	journal.ppat.1004419	null	[ [ "Leishmania parasites have a complex life cycle usually alternating between an insect vector and a vertebrate host , or between vertebrate hosts .", "The parasite is spread to humans through sandflies of the genus Phlebotomus or Lutzomyia during a blood meal [1] .", "Within the mammalian host , Leishm...	[ "Infection of macrophages by the intracellular protozoan Leishmania leads to down-regulation of a number of macrophage innate host defense mechanisms , thereby allowing parasite survival and replication .", "The underlying molecular mechanisms involved remain largely unknown .", "In this study , we assessed epi...	[ "The L . donovani parasite causes visceral leishmaniasis , a tropical , neglected disease with an estimated number of 500 , 000 cases worldwide .", "Current drug treatments have toxic side effects , lead to drug resistance , and an effective vaccine is not available .", "The parasite has a complex life cycle re...	2014

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